Higher costs and longer waiting times, greater complexity in construction (might also suggest that there could be expensive breakages in the making of a multi-blade, not a pleasant scenario for a Custom maker) I also feel that many Custom makers favour developing a niche or particular skill, liking for certain patterns and dislike attempting the untried and untested. Who can blame them? Multi-blade knives, SAK excepted, are uncommon in Europe and this is also the case with Custom/Artisan makers. Whereas factory multi-blades have been popular in the US for over a century yet only very top Custom makers offer multis in the US, there are Japanese Custom makers who offer them, but at high cost.
A lot, but not all, factory multi blades have blade-rub, notably krinked patterns. Customers might not take kindly to blade-rub on a Custom yet it might almost be unavoidable, a slight mistake in tolerances and construction and there it goes...
Custom knives are usually expensive to very expensive but at the the same time I very much doubt that most custom makers actually earn a huge fortune from their demanding and exacting skills, this too might explain the preponderance of single blades.