I understand the OMNY card and retail model is coming soon but it is still more convenient to do PAYGO with one card as opposed to two.
Regarding the tap issue, I had that happen on Saturday on the Q53 with a free transfer. Tapped, confirmed, but it didnt show up on the site for a day or two. And once it did, it was listed as Other Route instead of Q53. No issue with tapping the following day, showed up right away (free transfer also).
On the TAB (transit court) site , there is a space for OMNY account numver on the appeal form to counter this issue. Though to be fair metrocard has the same provision on there.