Most of the boot is covered by the greatcoat, so if you want to paint on gaiters on some then it's no biggy.
As it is that set is very poorly set up for early/ mid war anyway. I bought one for spare bits years ago and there aren't enough Kar. 98 rifles. Instead there's an abundance of Stg.44s, Gew 43s and MG-42s along with a host of panzerfaust. Boots aside, it's really aimed at late war anyway.