(Author of the spec here)
A fixed-size Merkle tree is a great idea if we wanted to sync the entire set of messages between distributed MX destinations. In fact, we should probably consider that approach for our server <-> server replication. However, JMAP is aimed at client <-> server sync. There are a number of different issues to consider here. The client may have limited or no cache (a webmail app for instance must normally start anew each time, and needs to efficiently fetch just what it needs; if we had to wait for a 60GB mailbox to sync every time we loaded our webmail, well, obviously that's not going to work. A mobile mail client often only wants to download the first few items in the mailbox given the current sort order so it can display them to the client. The JMAP spec allows a client to download, say, just the list of the first 50 messages, newest first, in the Inbox (single round trip). Then, at a later point, it can ask for and receive a space-efficient delta update of what has changed within those first 50 messages in the Inbox, regardless of how big the Inbox really is, or what other messages may have been delivered elsewhere (including lower down the Inbox, but outside the top 50). Again in a single round trip. This is really powerful: you can see that by comparing the refresh time of a folder in the FastMail mobile web app with the iOS or Android native mail app (over IMAP); the mobile web app is much quicker.
The other thing to remember is that the metadata about the message is mutable, and needs to be kept in sync as well. Again, the modseq system described in JMAP allows this to happen efficiently. If you have a distributed server system with multiple masters, you will again use a different system to keep those in sync (as they each assign new modseqs, whereas the client does not). However, this too can be dealt with relatively easily: if the modseq for a message differs between two masters, it must be set on both to max(the higher of the two modseqs, the next highest global modseq on the server with the currently lower modseq). This will ensure that both will end up in the same state, and that the client will get refresh its state for that message if it has to, no matter which master it last synced with.
So essentially, there's a difference in what you want in a protocol for server <-> server synchronisation for distributed mail backends compared to client <-> server sync for mail apps. JMAP is focussed on the latter, but tries to make sure it doesn't include assumptions that severely limit the former. The spec does not require a particular format of message ids: they do not have to be based around IMAP's ascending UIDs (although the sync algorithm for partial mailbox listings may be slightly less efficient if not).