Well I shipped fat jars using capsule more than 15 years ago without any issues. Nobody ships file-trees.
Also the Startup depends on how much memory you allocate, but much of it is due to verifying class security, a feature that other runtimes don't even have. Or badly used reflection, another feature others don't have.
In any case I really never found it an issue if a server takes 3 seconds to start and I never understood why people complained about Java startup. My guess is they complain about clunky desktop application with a million classes written in it.
Regarding the bytecode: the interpretation and just in time recompilation gives Java sometimes better than native performance.
It also allows you to hook into the code on the fly and transform it with agents. Can native do that?