You are correct, Mailpile does not synchronize with the IMAP server. It downloads and optionally deletes from the server.
And yes, this rules it out for some users. Someday this limitation will be addressed, but it’s a big task and until then we just have to smile and encourage people to use other tools if this matters to them.
Our intermediate “mitigation strategy” here, is to make sure the Mailpile web UI is accessible over the Internet (even for home installations), so you can interact with your home Mailpile from your phone, or from work. This reduces the need for multiple mail clients.
One of the reasons this strategy was chosen, is because multiple mail clients and PGP encryption really don’t play well together. Copying keys all over the place and managing them is not fun for mere mortals. If we want to actually make progress encouraging people to use PGP for all their mail, we need to solve the remote access problem and allow them to abandon all the mail clients that don’t do a good job with encryption.
I hope this clarifies a bit and explains why things are this way.
Edit: Just to clarify, as I write this the remote access stuff is still a work in progress. You can roll your own using Tor hidden services and/or PageKite (or good old fashioned port forwarding), but the goal is for both to be a button-push away, even for non-technical users.