I think it's a problem that will only affect you for a relatively short time. Once you have a few million you can fly somewhere interesting, buy a mining hauler or combat viper to do the interesting task/community goal, sell it when you are done and move on. I didn't bother transporting my combat viper from founders world to Ngaiawang. I just flew there in my T6 (which has much better jump range) and bought one there. When I'm done I'll sell it and lose 20k or so, but that's not a big deal.
If I want to have a fleet of expensive ships, I'll station them at Founders world, where I have the discount anyway.
The other model to consider is that if you have a big expensive ship, that's your home, rather than any specific station. If I was flying a python or anaconda about I'd think of it that way. In a given region I might buy a smaller ship for a specific task, then sell it again and start my nomadic travels again in my mobile home.
Options to consider. The sidewinder ferry also works, but only if you don't move your main fleet base very often and your fleet is small.