Syn 1 indirectly incentivizes you to wait for cooldowns to refresh and hp to regenerate before starting tough fights. Standing still behind walls, hidden from enemies. During this there is no threat, as rooms are not on timers and enemies hunting you down if you take too long are very easy and very hard to trigger even, a good example is the LD room before fighting the two tanks where it is optimal to go in at full strength but you could be waiting for minutes at a time for your health to come back.
Similar is finding bolts and heart core pieces, but this is much less core to the experience and not as harmful. If you miss them during regular room clearing it is optimal to go back and find them, but this is uninteresting with no threat after the room is cleared
Im no game dev so I cant claim to know the solution, instead I will give examples on how other rogue lites tackle similar issues. These games are radically different from Synthetik so I would never, and do not, suggest carrying them over 1 to 1 into Synthetik.
In Enter the gungeon and Binding of Isaac item cooldowns are based on combat, except a few, they will cooldown as you deal damage or clear rooms, never with time. Idling to wait for cooldowns grants you nothing
Risk of rain scales difficulty with time. Forcing the player to choose between fast play or getting upgrades which takes time. In Syn 1 it is always better to find those bolts and heart cores than not, searching for them before the floor is done is only a choice between smooth gameplay into next room or cleanup chore.
Spelunky spawns an indestructible unstoppable mob if you take too long. To discourage harmfully optimized gameplay like farming each and every enemy with life leeching items. This exists in Syn 1 but it is barely a threat. It would be thematically fitting for the Machine legion to corner you with squads of ultralethal assasination machines should you give them enough oppurtunity to figure out your position.
HP regen is fundamentally an issue, if you apply the combat-only cooldown system to it it merely becomes life leech. I would suggest complete removal of HP regen and replace it with another health recovery system such as making enemy health drops much more effective or, adding valuable Medikit items that can be held onto until a set amount and then used at a button press. Medikits can be combined with a hp regen system as in Far Cry, where regen is fast to prevent downtime but only regens upto a percentage of your health that decreases as you take more damage, a Medkit must be used to unlock the taken away percentages.
Clearly, these downtimes are not easy to fix. They need vast overhauls of the game's systems. I hope the effort is made, I believe a look at downtimes would substantially increase how smooth the game plays