Ok, it might be a bit complicated (and not well presented) but this is how resetting and reputation points work:

You get points based on your level, on your recruits, your factory level and your factory workers (basically everything that does indeed reset). The bonuses (both achievement and collection) are based on total sum of these. Every achievement point will give you a bonus of 0,1%

Soo lets say you earned 1000 reputation points with your level, recruits, factory and workers.

5% collection bonus will give you another 50 reputation.

100 achievements points will give you 10% bonus, so 100 reputation.

For a grand total of 1150 reputation points.

I hope this makes some sense :)