Enabling cron by default should be possible by adding an entry to the appropriate script. I see that there is an entry in
/etc/rc.local to start the cups service. I presume, but have not tested, that adding cron to that same file in a remastered version will thereafter ensure default starting of cron at boot. But I have cause for doubt after reading section 11.6 of the
Debian FAQ - does the same apply to Knoppix, I wonder?. Perhaps you can run some tests and let us know, or someone with definitive knowledge will chime in.
Try starting cron within your persistent install and rebooting, then check whether cron remains running (for example, by scheduling a command and seeing whether it executes). If persistence keeps cron running, then your synchronised remaster will probably do the same.