you get notifications of apps like they synced without VPN
This sounds abnormal. Did they actually sync, or could it be an app bug that reports a sync even if it didn't?
It could also be that OpenVPN authenticates correctly, but reports it to you a bit late, so the app looks like it synced without VPN but actually didn't.
One easy way to know for sure is to simply use a bad username/password on OpenVPN. This means OpenVPN cannot connect to the VPN server, and Android should never get Internet. Ideally, if you control the OpenVPN server, just make it so your traffic never goes to Internet, it's relatively easy if you have e.g. pfsense/opnsense.
The app that supposedly synced, can you make it so that you can check that it actually synced?
E.g. put your phone on Airplane mode, then (if the app is Signal) then ask a friend to send you a Signal message, then turn off Airplane mode.
OpenVPN should be the only connection Signal can use to get the message, and it will fail on purpose (since you have a bad password, or if you control the server and deny Internet). If Signal gets the message, then it sounds like a serious bug you should report to Google directly (https://issuetracker.google.com/) or at least to GrapheneOS team (https://github.com/GrapheneOS/os-issue-tracker/issues/).
If the app (Signal in my example) does not actually sync, then the app has a bug where it can report syncing even if it doesn't actually sync.