However, since LISA OS came with an integrated tools package (as in "7/7") turning the tools into components (to be used by universal documents) would have posed less a problem. I think, it's really the third party aspect that doesn't match the model.

Yep. The only way this could work in a real-world sense would be for it to be the OS, and for the OS to be purpose-built to function this way from the start. Completely extensible, completely communicative between modules (and good luck with that), completely a security nightmare.