Okay, I thought I'd try this again, I bought two identical PNY Turbo Attache 4 USB 3.0 16GB flash drives, one is formatted with reiserfs overlay partition and the other is fat32 overlay file,

So let's do the same operation:

The reiserfs partition overlay:

Code:
knoppix@Microknoppix:~$ time sudo dpkg -i mamepackages/mame_0.189+dfsg.1-1_i386.deb mamepackages/mame-data_0.189+dfsg.1-1_all.deb 
dpkg: warning: downgrading mame from 1:0.186-dmo1 to 0.189+dfsg.1-1
(Reading database ... 451601 files and directories currently installed.)
Preparing to unpack .../mame_0.189+dfsg.1-1_i386.deb ...
Unpacking mame (0.189+dfsg.1-1) over (1:0.186-dmo1) ...
dpkg: warning: downgrading mame-data from 1:0.186-dmo1 to 0.189+dfsg.1-1
Preparing to unpack .../mame-data_0.189+dfsg.1-1_all.deb ...
Unpacking mame-data (0.189+dfsg.1-1) over (1:0.186-dmo1) ...
Setting up mame-data (0.189+dfsg.1-1) ...
Setting up mame (0.189+dfsg.1-1) ...
Installing new version of config file /etc/mame/presets/gameboy.ini ...
Installing new version of config file /etc/mame/presets/gba.ini ...
Installing new version of config file /etc/mame/presets/lcd-matrix.ini ...
Installing new version of config file /etc/mame/presets/lcd.ini ...
Installing new version of config file /etc/mame/presets/raster.ini ...
Installing new version of config file /etc/mame/presets/vector-mono.ini ...
Installing new version of config file /etc/mame/presets/vector.ini ...
Processing triggers for desktop-file-utils (0.23-2) ...
Processing triggers for gnome-menus (3.13.3-9) ...
Processing triggers for mime-support (3.60) ...
Processing triggers for hicolor-icon-theme (0.17-1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Processing triggers for menu (2.1.47+b1) ...

real    18m34.462s
user    0m9.199s
sys    0m7.050s
knoppix@Microknoppix:~$ time sudo dpkg -i mamepackages/mame_0.186-dmo1_i386.deb mamepackages/mame-data_0.186-dmo1_all.deb 
(Reading database ... 451579 files and directories currently installed.)
Preparing to unpack .../mame_0.186-dmo1_i386.deb ...
Unpacking mame (1:0.186-dmo1) over (0.189+dfsg.1-1) ...
Preparing to unpack .../mame-data_0.186-dmo1_all.deb ...
Unpacking mame-data (1:0.186-dmo1) over (0.189+dfsg.1-1) ...
Setting up mame-data (1:0.186-dmo1) ...
Setting up mame (1:0.186-dmo1) ...
Installing new version of config file /etc/mame/presets/gameboy.ini ...
Installing new version of config file /etc/mame/presets/gba.ini ...
Installing new version of config file /etc/mame/presets/lcd-matrix.ini ...
Installing new version of config file /etc/mame/presets/lcd.ini ...
Installing new version of config file /etc/mame/presets/raster.ini ...
Installing new version of config file /etc/mame/presets/vector-mono.ini ...
Installing new version of config file /etc/mame/presets/vector.ini ...
Processing triggers for man-db (2.7.6.1-2) ...
Processing triggers for menu (2.1.47+b1) ...
Processing triggers for hicolor-icon-theme (0.17-1) ...
Processing triggers for desktop-file-utils (0.23-2) ...
Processing triggers for gnome-menus (3.13.3-9) ...
Processing triggers for mime-support (3.60) ...

real    19m0.710s
user    0m7.928s
sys    0m2.538s
knoppix@Microknoppix:~$
The fat32 file overlay:

Code:
knoppix@Microknoppix:~$ time sudo dpkg -i /mnt-system/mamepackages/mame_0.189+dfsg.1-1_i386.deb /mnt-system/mamepackages/mame-data_0.189+dfsg.1-1_all.deb 
dpkg: warning: downgrading mame from 1:0.186-dmo1 to 0.189+dfsg.1-1
(Reading database ... 451601 files and directories currently installed.)
Preparing to unpack .../mame_0.189+dfsg.1-1_i386.deb ...
Unpacking mame (0.189+dfsg.1-1) over (1:0.186-dmo1) ...
dpkg: warning: downgrading mame-data from 1:0.186-dmo1 to 0.189+dfsg.1-1
Preparing to unpack .../mame-data_0.189+dfsg.1-1_all.deb ...
Unpacking mame-data (0.189+dfsg.1-1) over (1:0.186-dmo1) ...
Setting up mame-data (0.189+dfsg.1-1) ...
Setting up mame (0.189+dfsg.1-1) ...
Installing new version of config file /etc/mame/presets/gameboy.ini ...
Installing new version of config file /etc/mame/presets/gba.ini ...
Installing new version of config file /etc/mame/presets/lcd-matrix.ini ...
Installing new version of config file /etc/mame/presets/lcd.ini ...
Installing new version of config file /etc/mame/presets/raster.ini ...
Installing new version of config file /etc/mame/presets/vector-mono.ini ...
Installing new version of config file /etc/mame/presets/vector.ini ...
Processing triggers for desktop-file-utils (0.23-2) ...
Processing triggers for gnome-menus (3.13.3-9) ...
Processing triggers for mime-support (3.60) ...
Processing triggers for hicolor-icon-theme (0.17-1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Processing triggers for menu (2.1.47+b1) ...

real    4m31.019s
user    0m8.833s
sys    0m5.901s

knoppix@Microknoppix:~$ time sudo dpkg -i /mnt-system/mamepackages/mame_0.186-dmo1_i386.deb /mnt-system/mamepackages/mame-data_0.186-dmo1_all.deb 
(Reading database ... 451579 files and directories currently installed.)
Preparing to unpack .../mame_0.186-dmo1_i386.deb ...
Unpacking mame (1:0.186-dmo1) over (0.189+dfsg.1-1) ...
Preparing to unpack .../mame-data_0.186-dmo1_all.deb ...
Unpacking mame-data (1:0.186-dmo1) over (0.189+dfsg.1-1) ...
Setting up mame-data (1:0.186-dmo1) ...
Setting up mame (1:0.186-dmo1) ...
Installing new version of config file /etc/mame/presets/gameboy.ini ...
Installing new version of config file /etc/mame/presets/gba.ini ...
Installing new version of config file /etc/mame/presets/lcd-matrix.ini ...
Installing new version of config file /etc/mame/presets/lcd.ini ...
Installing new version of config file /etc/mame/presets/raster.ini ...
Installing new version of config file /etc/mame/presets/vector-mono.ini ...
Installing new version of config file /etc/mame/presets/vector.ini ...
Processing triggers for man-db (2.7.6.1-2) ...
Processing triggers for menu (2.1.47+b1) ...
Processing triggers for hicolor-icon-theme (0.17-1) ...
Processing triggers for desktop-file-utils (0.23-2) ...
Processing triggers for gnome-menus (3.13.3-9) ...
Processing triggers for mime-support (3.60) ...

real    2m3.485s
user    0m7.394s
sys    0m1.280s
With the reiserfs overlay partition, both operations take 37 minutes,
with the ext2 fat32 overlay file, both operations take around 7 minutes.

So reiserfs is about 5 times slower in this case.

It's pretty clear that you want to use the overlay file when you install to a flash drive.