Does anyone have any recommendations on how to maintain flows in SFDX projects?

Our current continuous integration pipeline looks like this:
Create Scratch Org -> Make Changes -> Check In -> PR into Master -> CI Server Builds and Deploys to QA sandbox using sfdx mdapi:deploy

Unfortunately, as soon as we added flows to our repository / scratch orgs, we started experiencing build failures as those flows already exist on the QA server after the first deployment.
Is there a workaround for this or do we just need to exclude flows from our automated builds?

We have a web app that uses salesforce Communities as IDP to register and authenticate users via OAuth 2.0.
Set up connected app for this with correct OAuth settings, redirect URL for testing with http:localhost NOT https yet. Wen use connected app in mode all users are Perauthorized with admin (avoid that Authorize app poopup). We set startURL parameter to eredirect user to our web -app after Community login or register.
Login existing user works as expected user authenticates and redirected to the app with Access token - GREAT!
Now Registration new user - DO NOT WORK. It seem new user is created but automated-login for this new user always redirects user to Community portal Home page. Even we set StartURL to our direct to http://localhost:8080... still Community page. Try to change APEX controller to force redirect still not working. Site.login method seem to NOT responding to startURL when Connected app is set PRE AUTHORIZED.

On other hand if I switch connected app to Allow all users to Self authorize then Site.login redirects to our Web-app via startURL.

Is this some Limitation that makes use of connected app with web-apps painfull? Bad UX requiring some additional steps.
May this is some Comunity bug? Any insight will be helpfull.
Thank you