I agree with you that it did not appear that your milk kefir poolish and dough were fermenting too quickly. However, I thought that it might be worth trying some diastatic malt to see if more sugars can be produced by the added diastatic malt. Diastatic malt acts on damaged starch and, although I would expect that the barley malt added to the flour is balanced against the degree of starch damage in the flour, if there are enough sites for the diastatic malt to work on maybe there will be more natural sugars released from the damaged starch. Up to this point, I had been counting on the lactose in the milk kefir to contribute to crust browning. Maybe there isn't sufficient lactose to accomplish that purpose and/or there is something that is consuming the lactose, such as friendly bacteria as was discussed earlier in this thread at Reply 49 at http://www.pizzamaking.com/forum/index.php/topic,12173.msg115232.html#msg115232
There are other ways of trying to increase the degree of crust coloration, such as using different forms of sugar and dried dairy whey, which is rich in lactose, but I would rather defer those possibilities pending the results you get from using the diastatic malt.
You mentioned that you used diastatic malt for the Montreal-style bagel dough that you made using the milk kefir in lieu of the commercial yeast. In widespreadpizza's bagel dough formulation, the only form of malt that I saw was non-diastatic barley malt (dry or liquid). Did you use the diastatic malt in lieu of the non-diastatic barley malt product, or did you supplement the flour with diastatic malt while still using the non-diastatic malt? That aside, I would fully expect the eggs to contribute to final crust coloration, making it difficult to isolate the independent crust browning effects of the eggs and malt.
Some time ago, either a member used the basic Lehmann NY style dough to make bagels or suggested that possibility, so to reverse that process and use bagel dough to make a pizza might work.