I agree. More and more...I'm finding you only need to balance the rim. The rubbers are so close, it doesn't make much difference.
Regarding the dots - if they're there, I'll certainly match it to the heavy spot of the rim.
The rim should have come with a paint dot from the factory - inside and outside. I've seen several where it was a few inches away from the valve stem. I balanced the rim w/o a tire to verify. I've also found the mfg. puts a paint dot inside the rim...so if you have cleaned off the outer dot, you may still find it after you take off the rubber. Just paint another dot on the outside and your good to go. If you don't like that idea, get a crayon and mark it while you have the rubber off.
If you take the time to align the dots, you'll get a smoother ride - imho - or...you'll just ride with greater peace of mind.
Plus...I think it's good for an extra 5-10hp!
RTG