I agree that I think the main issue comes down to the larger players using reasonable judgement in who they hit, in assisting the community to grow. I don't think it should be an admin enforceable rule that wood/stone bases should be left alone, because I agree that there may be some players that abuse that by building solely out of stone and wood and then crying, "but I was only in stone/wood! You broke the rules by attacking me!" Even though I find this highly unlikely, as those tribes would be marked as cowards and targeted in other ways most likely, the possibility of this abuse existing is why I don't think it should be a 'rule'. There are many variables that can hinder this and people are always out to exploit what they can to get ahead. It will only give Munki more headaches.
Because of this, it should really just come down to judgement from the larger tribes. If you see a tribe you're unfamiliar with that is in a 4x4 stone base with a raptor, trike and couple of pteras, it doesn't take a brain surgeon to deduce that there's a high chance that they're a new player and not worth hitting (don't have loot better than what you currently have). If however that same tribe has been on the server for a while and is active, then there is a higher chance that taking a peak into that stone base might find a metal core with decent loot inside. Developed tribes that are hitting smaller stone/wood bases on the off chance that they MAY have good loot, is what is contributing to driving some players away. It's obviously different if that smaller tribe started something with that larger tribe, but I'm not talking about those situations.
At the moment the only way I've been trying to combat this issue is to help out newer players where I can, offer a 'safe' (ish) place in the south with communal forges/chem bench/smithy/crafting station etc. for a new player (or player who lost their gear in a raid) to make stuff for themselves and get a flier, and to remind smaller/newer players that it's in their best interest to leave things like smithys/forges/certain boxes etc. unlocked inside their bases so that raiders are not forced to destroy it just to check what's in there. I know that when I see loot I'm not interested in, I leave it. If I'm forced to destroy the box/smithy etc. then all I can do is MAYBE leave a box nearby and fill it with the stuff so it doesn't despawn. But that comes down to time, the pvp I'm encountering and a variety of other factors which results in raiders not usually doing that. Not all smaller players leave their gear unlocked inside their bases, which results in their gear being destroyed which makes it harder for them to recover from a raid, but if the 'alpha' tribes in the cluster at least move their attention from these kinds of players, it'll hopefully reduce the frequency of it happening. For this cluster to grow, players need to be going for targets closer to their tier more often than what we are currently seeing.
I'm tired and hungry so not sure if this rambling has made much sense but eh