@Gil_Sharon, I don’t follow which one is the possible discrepancy but I think your concern is that now your feature table will have a subset of the features that are in your tree. If that’s the case, that’s not a problem at least for the regular stuff that we do with the tree (like UniFrac or Faith’s PD) as those not included tips in the feature table are ignored, which should be the case for all methods I can think of. Again, I guess it depends on your algorithm.
Just to be clear, the other way around, might be a problem (features in your feature table that are not in the tree), which we normally consider noisy sequences but we also know that nothing is perfect. The current thing we do is to simply remove them but this is a case by case decision.
Perhaps useful, here is a list of commands for Transferring Qiita Artifacts to Qiime2.