It should work, throw the github url for an app into obtainium and try updating. It should update and keep the settings.

If this fails, I'd say one time obtainium setup would be required. No need to get everything through obtainium (do amethyst as it updates frequently and runs ahead of fdroid a lot).

Much of stuff you'd have installed through aurora would not be open source and if it is you should use fdroid/github versions as they'd lack the Google components. Use aurora for apps that are not available elsewhere, better than sourcing apks on shady websites. Aurora pulls from Google directly so at least they are as published by devs.

Do try neo store/izzysoft repo combo for most of you fdroid installs, it'll take over updating without issues for fdroid installs.