I don't understand that argument (and I've heard it several times), see comment below about plugins dependencies. I.e. that argument is OK for isolated cases, not for more complex dependency graph.

This is the reddit thread where the lead of the project talks about it:

https://www.reddit.com/r/neovim/comments/1n2nax0/why_vimpack...

It doesn't answer your question about plugin dependencies (although vim.pack lets you handle this), but it might give you more insight on where vim.pack will go in the future.