Should I use 'by' as a preposition of time in past/future perfect tenses only?
In that sense, you can use 'by' with any tense. Consider its meaning as given by the Longman dictionary:
Before or not later than a particular time.
Examples:
- The document needs to be ready by next Friday.
- By the end of the day we had sold over 2000 tickets.
- By the time we got home we were tired and hungry.
- I'll be home by 9:30.
- Please try to have this done by Friday.
All the examples are borrowed from the Longman dict. so you can trust them.