Yes, I know what you mean. For the purposes of counting while learning and getting the note groups in your head and under your fingers, I would probably count as you suggest as if in 4/4 time.
What I actually do in face to face lessons is count it as:
1,2,3,4 1,2,3,4 2,2,3,4 2,2,3,4 so as to emphasise the 2 main beats of the bar. Whether that actually helps I don't know, but I'd suggest counting it as 4/4 whle you get used to it.
If I'm not making much sense send me a PM for further clarification :)
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