Run unison in background on startup?

Why not to point Apache to your shared folder on VM in the first place? This is as simple as to add/change one file for your virtualhost (I believe you've done this anyway). This will let you not to wait 5-10 seconds while your server document root is being updated.

However what you actually ask is a periodically running some command, so in the end you just need a cron job. This answer may be helpful for you.

So you just add to your crontab file:

* * * * * unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1
* * * * * sleep 10; unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1
* * * * * sleep 20; unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1
* * * * * sleep 30; unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1
* * * * * sleep 40; unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1
* * * * * sleep 50; unison -batch -owner -group /folder1/ /folder2/ >/dev/null 2>&1

The >/dev/null 2>&1 means to redirect stdout and stderr output i.e. remove all logging.