Is cosigning / joint signing not an option?
For apps not enrolled in the Play Store signing scheme, the phone actually verifies directly against the publisher's key, that Google now wants to relegate just as an "upload key". I am saddened by Google's efforts to undermine this fundamental OS security feature. The ultimate goal is clearly to kill off any chance of competing app stores, as developers of new apps distributed through Play Store can now actually never access the key that's supposed to show they control the app, no matter what channel it was delivered through (e.g. Play Store vs. F-Droid.. Really bad for new Open Source apps!)
I do know a bit about PKI. And one option might be that the workflow be something like:
Dev signs bundle => Google signs bundle (including dev signature) => User/Client verifies both signatures.
Google are still signing here, but if the dev signature doesn't verify (or isn't present), there's a post-build modification occurring, which is the principle issue raised in the tweet thread.
While APK backups aren't officially supported and therefore might not factor into the decision making, curiously enough Google itself only recently added a feature to the Play Store which apparently allows direct sharing of APKs between nearby devices. Split APKs however mean that you can only sensibly share apps with devices having the same screen density, language, etc. as your own device, somewhat devaluating that feature again.