It still depends on how long the attribution is set for.... and what time frame you are looking at.... If you are set for 30 day expiry, then looking at this or last month on your reports, you should be fine as the windows would have cleared already... but if you are looking at the last year, then yeah, you can end up with some odd mis-matches when rules were modified.
As for breaking down your Marketing Channels by Referring Domain, remember that those have different attributions... Marketing Channel is likely to be 30 days (but you may have changed this in your settings), but Referral Domain is definitely Visit level attribution.
But, if you use the Marketing Channel Instances metric, this should only be when a marketing channel value was set, and then your Referring Domain should also be the one as recorded when the channel was set. Basically this should compensate for the attribution mis-match, because you are no longer looking at 30 (or custom) days against all visits, but looking specifically at visits where the channel was set.
could you share the basic dimension / metric structure to look at that?