Unfortunately I don't have good news.
I went with automatic dependency collection for APIs and Initialization>Get[...] in cloud notebooks.
I am fortunate that there isn't anything fancy in my code like working with the LibraryLink, external data/caching or whatever.
While I don't like it didn't cause any problems except I would gladly shave those few milliseconds associated with loading.
And afaik there is no solution. Even with the EPC you'd need to restart it which is hardly a convenient solution.
