I will concur on the point with limiting maximum colony player size with resolving colony crises and though I don't think it would fundamentally fix the problem, it will definitely help reduce the easily accessible mad profits.
the issue is this adds an obtrusive feature that the player has to get around
the worse part of which is, you have to wait for the crisis to trigger before you can solve it which is a lot harder if your locked to size 3's till you beat one as crisis's tick a lot slower the smaller you are.
to oversimplify we are half fixing colony engagement being "start colony and then wait for money printing" by just adding even more waiting, which doesn't actually fix the issue, it just kicks it down the road a bit.
I can agree with those above that suggested disconnecting accessibility from profits, and i can agree. while it can be argued that it should have some effect, there's always going to be a limit of how much it helps because eventually you're getting to transport being free, and it's not like cheap transport can make the production of that item any cheaper if all the things going into are already on site.
so disconnecting accessibility from profits does make a lot of sense and in part removes the super money printer colony issue because most of the issue is everyone is boosting their colonies to 200% profit with that.
I do however heavily disagree with OP's view on generalist colonies that put multiple steps of a production chain on one planet, that should not increase logistics cost, that should reduce it seeing as the materials are already on site when they are made. it takes a lot less effort to ship locally around the planet then to ship it around a solar system or to an entirely different star system.
Instead, i suggest making some systems to give the player other options to sometimes give them a reason to not make EVERY colony a generalist, seeing as outside of high hazard worlds you pretty much have every reason to make every planet a generalist, especially with growing industry limits, its just weird not to make use of those slots to make more production and thus more profit.
Put more specifically we could use a way to expand an existing industry to take up multiple slots for even better production at a more efficient upkeep then having two planets running the same industry. that would give some incentive to make at least some planets specialized to make use of these bonus's, especially if you start throwing in colony items.
this would also in a way assist ludic majority as well, as at this time once you reach a large enough size of colony to have 4 industries, sticking with ludic majority actually can be detrimental to the effectiveness of that world as you no longer utilize the maximum output of that world. being able to build even larger farming/light industry would help fill that hole.
on an aside i would like to toss in the ring the importance (or lack thereof) of resource ratings on a colony planet. More specifically the larger a colony gets the less it matters. when you have a size 6 the difference between sparse ore and abundant ore is insignificant at best. and generally, only matters on brand new colonies. after that only hazard really matters at all. having resource values be a multiplier instead of a flat effect would flip things around to mattering a bit less on a new colony but having a large impact on a large one or, perhaps there is some in-between option i have not thought of at this time idk.
ps. i agree with Megas, tech mining really needs some love, it has almost no value to the player except hope of maybe getting lucky and getting a bp or two. even then you almost never get blueprints from it (even on the largest of ruins), and the other outputs from tech mining are so tiny there's no real benefit from building it. pretty much a waste of the player's time.
