Hi, I usually don't do suggestions, as I can imagine that the work load might already be well enough of maintaining projects for anything outside of personal use - so feel free to ignore if it's outside of scope, real life, or straight up desire.

That said, I feel like a dedicated machine for packing stuff into crates could do this mod well. To save on time, you could simply re-use the assembler model (if that's alright with Factorio's modding licence, idk), and then just have it accept a wooden crate + 2 stacks of an item (kinda how furnaces accept ore without you needing to set recipes for each new ore)

Having one of these on ground would allow one to logistic all requested space delivieries through a packer, and then on the space ship, logistic all crates through an unpacker automatically.

It's just an idea I had, and I don't know if it's doable (after all furnaces only require one different type of material... unless you made it a reskinned furnace and set crates as the only acceptable fuel type...???) but I wanted to suggest it anyways :D