Thank you — it's clear you're thinking in whole systems rather than isolated tweaks. I'll answer each point honestly, including the parts I won't be doing.
Multiple platforms — no, and this is the most fundamental "no". A single ship that is your base is the mod's core bet, not a sign of something unfinished. Everything else follows from it: why you can't build on planets, why there are no rockets, why losing the ship is frightening. A fleet of specialised vessels would be a good game, but a different one, and building it on top of this would mean rewriting the UI, the missions, the trading and the hold — and ending up with a mod that makes this one redundant.
One observation about 2.1. The logistics expansion there is built almost entirely on the "planet → rocket → platform" chain — smarter planet requests, mixed rocket payloads, drop slots. We have no rockets at all and no way to lift cargo off a surface, so of that whole package essentially only platform-to-platform transfers in the same orbit apply here. The payoff from multiple ships is therefore much smaller in this mod than in vanilla.
Speed and weight — you're right in substance, with one correction. The vanilla acceleration formula does already account for weight: it sits in the denominator. But weight has almost no effect on top speed — only through the 1 + weight/10,000,000 factor, which at realistic masses amounts to a few percent. Top speed is set by thrust balancing drag, and drag scales with width. Hence the vanilla meta of long, narrow ships — your diagnosis is accurate.
That formula is an ordinary utility constant, and a mod can rewrite it in a single line, so there's no technical obstacle. But in our case a weight penalty hits the wrong target: our ship is required to be heavy — it's a factory, a warehouse, a greenhouse and living quarters all at once. Penalising weight means penalising the very idea of playing with one ship. Ship classes make sense when you have several ships — which makes this proposal inseparable from the first one.
Planet orbits for focused mining — same reason. A dedicated mining ship parked in orbit only makes sense with a fleet. Here, resources come from the route, and sitting still means not playing.
The trade hub in the middle, though — that's an excellent idea, and I'm noting it down seriously. It's the only one of the four that requires neither a second ship nor changes to flight physics, and it fits exactly onto what the mod already has: markets with different stock per location, reputation, missions, research-gated access. Routes a quarter longer so automatic pathfinding avoids it is an elegant solution, and the gravity-assist explanation appeals to me. Special stock and its own missions would sit very well there. I won't promise a timeline, but it goes onto the candidate list in exactly that shape.
Thanks for the analysis — it's useful even where my answer is "no".