Modest W15 is out, and the two most annoying bugs seem to be fixed:
1) No Internal Errors (yet)
2) Mail read in Modest is marked read on the Google IMAP server

Interestingly, after installing this version, I ran Modest and got a dialog about trying to connect to Google IMAP with an unauthorized? unknown? (I forget) certificate. I clicked on "yes" or "OK" or something and then it downloaded my e-mails. It also didn't start doing background checks until after that, too. It was only after I had cleared the dialog that I realized I should have written down what it said to report here.

The release notes for this version specifically say that they've fixed some background checking errors.