In those rare cases that an Affinity is gained in-play - recalculate the XP total to get the right result (so NEW TOTAL * 1.5 = OLD TOTAL). Yes, it means that XP is technically lowered, but not really. And you can then proceed to calculate the art/ability score with no hassle as the character gains more XP.
Either that or collecting fractions is how I prefer it.
Well, I take comments from the table under advisement. But I don't find it particularly compelling to add an affinity after any old Twilight Episode. Maybe after several in a row, particularly if some have turned out negative. And I doubt a troupe, as a whole, would be handing out affinities on a regular basis, but I might be wrong about that.
As it happes, consensus generally prefer handing out odd-but-potentially-useful out, rather simple and obvious bonuses.
That doesn't change the point though.
My "solution" is to not be bothered by an extra half of an xp a few times per year (often times twice in the same season if they're getting exposure through lab work). It is what the rules say, it generally makes the players pleased, and affinity while being a fairly powerful virtue still isn't game breaking.
The problem folks have with it could (I suspect) be better solved with a change in perspective rather than a change in rules. Of course that doesn't help metacreator at all.