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It seems SP's alliance with CHP-IYI did not help since at 1.4% they were not able to qualify in any seats anywhere, even in Istanbul. So we can view 1.4% of the 33.3% of CHP-IYI-SP as wasted.
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Looking at the preliminary seat distributions in each province they only make sense when applying d'Hondt to the alliances and not to the single parties. Therefore the 1.4% of SP still count for CHP and IYI.
I'm surprised about this myself because before the election I already wondered about this, but wasn't able to retrieve any confirmation and therefore assumed that d'Hondt would not be applied to the alliances as a whole.