All it would take is some with physical access and everything your faction has is borked.
Not really. The scope of the game limits what a single person can do - I don't think there's a loot decay or a 'delete' option to delete loot, but really I do not know how that is handled and can only guess. But even then, yes, if you let someone into your main loot room and they end up stealing everything (by you know, bringing in 100's of ships with 100's of shipping containers to fly away with all your loot), that's on you. Still, some reasonable restrictions (see, safe zone) for this kind of stuff should be in play, because well, hacks exist.
I don't even know how you would set up YOLOL to manage membership's ability to have factions pay for insurance when in built tools could do so much easier
Maybe you've heard the devs speak of a faction insurance system that pays members' insurance costs? I haven't heard this is a thing. If it's not a confirmed feature yet, then you're asking for the devs to program all this outside of YOLOL to achieve the same function, and hard-code it into the game to make it impossible/unlikely anyone develops any better way to deal with the problem. After all, what you're asking for in this feature alone, is to have someone else pay your insurance cost upon losing a ship or robot body - how can this not just be achieved by you know... someone handing you the credits? Taking away this player interaction is dangerous to a game. Many games lose out on the value of player-to-player interaction when it comes to trading and other currency interactions where it's more impactful to have someone actually hand you the thing/currency you need. Both methods have their pros and cons however a major con for having these faceless faction accounts is it removes the person/player from the action; you don't need someone else to help you, your uncaring, unthinking faction wallet takes care of it. And again, the whole feature needs to be created by the devs, given permissions and limits and who can access it and this all needs to be created server side to hold all the values and make sure no one can hack the values and so many other rabbit-hole 'what-ifs' surrounding any single one of these features.
There's adding fun gameplay and then there's stupid pointless grinding for features that other games dont make you do it yourself.
That's a huge misconception and I'm glad you gave me something to bite on here. Just because you, or I, don't enjoy some aspect of gameplay, does not mean someone else feels the same way. In other words, by restricting what is possible by forcing these dev-created systems into the game, you devalue the player who really likes to do those kinds of things (or might want to do those things due to the profit they make on doing it). If you simply carve out that no player can compete with the in-game systems you ruin a lot of gameplay from people who would really enjoy playing that kind of game. Every sandbox game has 1000's of different ways players play the game, and thus every single system you set in stone in Starbase becomes the only way that system can be done, and removes so many people from the equation.
I highly doubt you would not play Starbase if faction controls and permissions had to be programmed by every new faction. In addition to common, copy/paste code available to any faction within the first month, you also won't be creating a new faction with new permissions every day. It's a weird statement to see being made by you considering everything else the game brings - being part of a faction isn't even required.
Instead, I think about the large amount of people who, for example, do enjoy, or are good at, managing people; who would find their personnel micromanagement skills devalued if the game hard-coded this one specific way they can deal with their faction. Nothing is required, but giving players at least the option is better than forcing a system/feature upon players that will constantly not be good enough for everyone. Give the basic tools to the players, and let the players sort it out themselves, and the players will bring massive value to the game and they themselves will be valued by their team for their efforts in solving perceived problems.
It's easy to get tunnel-vision into thinking of what things you want (this goes for everyone, myself included, even devs), for yourself, for your own convenience and pleasure, and just say, "Surely no one else enjoys playing differently than myself," - I think that kind of approach is incorrect. Instead, consider the demographic and audience the game is aiming at - people who enjoy open world sandbox MMO games with FPS combat and PvP - and look at the whole scope of the potential players in that audience (it's massive, reaching almost every single game-player). Then, consider how any set system drives away some huge number of players, and decide if that feature is worth it, if it can even be done correctly. For example, the User Interface of the game is a set-in-stone system; but it will not appeal to everyone. Some will hate the "bland look", or find it unintuitive, or think some other game did it better, and those players will be driven away from the game because the UI just didn't make sense to them. Obviously, this is something the devs have to decide on - losing those players who don't like the UI is worth the cost, because everyone else who finds its theme satisfactory are vastly more numerous. In the end, I agree with
@Dusty in that there is a balance to be reached. Some things are worth the cost of loss of potential, and other things are not, and it's more about figuring out which ones maintain the most gameplay value.