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APKs can be end-to-end signed with keys under developer control. You can move between app stores or no store (data is preserved on update with same key). And Google can't fuck with it. (Well, they can fuck with the entirety of the rest of the phone, so that point's kinda moot.)
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For the past year, we've been using app bundles ourselves as part of GrapheneOS. We recently switched back to building an apk for Vanadium because Chromium's build system started tying unwanted things to whether it was an app bundle build. Issue wasn't with app bundles though.
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For the Play Store, the Play Store generates the apk and signs it, so they control the signing key. For existing apps, the developer still has the key too and the system supports key rotation so you could start releasing upgrades outside Play with the key rotated away from that.
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