Stripe support was of no help. After getting moved up the support ladder, the guy said to use the full domain instead of what the input field shows "example.com" or "subdomain.example.com". The Stripe system doesn't let you to use HTTP or HTTPS so I tried www.mydomain.com on profile #1 (I have two Stripe accounts/profiles with the same issue). On profile #2, I deleted the existing domain and re-added it as it was before (mydomain.com). The weird thing is that the records provided by Stripe are identical to my previously used ones. A day later, and both domains passed verification! WTH.
I suspect the BunnyDNS resyncing did the trick but took longer to fully propagate despite what online DNS checking tools report back. Maybe it was a Stripe cache issue too. If anyone ever hits this issue, do the following:
contact your DNS provider and have them resync your zones
delete your custom email domain in Stripe and re-add it.
As for the InvoiceNinja issues, my email delivery resumed after fixing the PDF generation issue that CR staff are looking into in another thread.