the issue of your just let your bot die is often better than return to base isn't what this topic is about. that one is also an issue, something that known to be hard to solve for long, and people were considering ideas like pickups, captured point converted to repair area, leech weaponry. however, increase respawn time to punish not returning to base, is not going to be one of them.
the issue we are talking about here is "things to be abused to lowering downtime". in addition this combined with bot with active modules with many charges or sheer secondary ammo capacity, can make very annoying builds. #1336900748541169676 message and here is one of my reason of why self destruct should not be prevented. so my suggestion is combat flag, respawn rate limit, parallel multiple timers.
you've made a long speech but your reasons don't conflict with what i said. and then how did you come to your suggestion of "using remaining hp percentage as the criterion of respawn time"? why remaining hp percentage of a bot should be measured for anything? why specific to self-destruct? you just saying "wont even notice 3 second difference", but only 3sec isn't making there's no deliberate punishment for using the self-destruct button; and if it really mean to be no big impact, then what are you even suggesting? from what i see, you don't even know what is being abused.