I totally agree with you OP and have thought this for a while. If you trade a player, you get a TPE; if you lose a player in FA, you get nothing. You get penalized for something totally outside of your control. And I agree that certain rules should remain in place, like needing to let your TPE/cap holds go if trying to get under the cap to sign another player. Maybe they could have a maximum number of TPEs you are allowed to have at any one time, as well.
I understand the small market/big market thing, but the luxury tax penalties are already extremely harsh - you just don't see teams doing what GSW is doing this year with Oubre very often. The more we see this done, the more of a discussion this might be in the next CBA.