Payment Apps which works on Custom ROMS

• Whatsapp Pay (Community said it)
• Amazon Pay (Community said it)
• BHIM (Community said it)
• PhonePe (I've personally tested it)
• CRED (Community said it)

Other resources:

https://xdaforums.com/t/guide-guide-for-how-to-use-banking-apps-in-rooted-devices.4630037/