>Concerning the problem of Clonks standing around - well, I hope we get some damage notification into the Clonk pictures so it should be possible to detect something happening

Sure, but you still could not control this extra Clonk

>But melee-oriented maps should not force you to have more than one Clonk anyway, imo

Look at CoFuT for example. Sure, simple melees (Minor Melee f.e.) don't need more than one Clonk at a time but there is more complicated stuff (like CoFuT) where Clonk management is a very important aspect (would you rather have a spare Clonk or risk a relaunch?) and limiting _every_ melee scenario to only having one Clonk just because the game lacks the possibility to protect those Clonks would not be very beneficial to the gameplay I think

>Protection in base

Sure, you could heal the Clonks slowly (which would be annoying in situations where you don't have an enemy and just want to go back into your mine without waiting three minutes for your Clonk to be recovered). But there will always be things where this doesn't help. Look at the CR rockfall-rule: One of those rocks can easily kill two of your Clonks if they happen to be hit by it - no slow recovery would every prevent this. And of course: You could say "hey, lets just make no rockfall rule for OC then!" and that surely is a point. But it would not enhance the variations of gameplay but limit them since everything that could inflict a lot of damage to not-controlled Clonks would be instantly imbalanced and not very much fun to play with

PS: I would rather weaken the strength of the base buildings so that an enemy can destroy them more easily if you find them to be a too ultimate protection at the moment
PPS: Or even give the Clonks the possibility to slowly deconstruct a building (if you have a weapon or a tool with you) which would deal damage over time and help against the situation of "haha, you are in my base but have no flints, I'm hiding in my base now"