I agree with you that the two methyl groups do make the alpha carbon somewhat less acidic, but the difference is pretty small. For example, imagine a ketone with a phenyl group on one side and a methyl group on the other. The pKa of that molecule is 24.7 (DMSO solvent and reference, 25 degrees C). If you change the methyl group to an ethyl group, the pKa is 24.4 (pretty much the same), and if you change to an isopropyl group, the pKa is 26.3. So it does go up, but not a whole lot. This should hinder whether or not you can form the enolate; you don't need to make the enolate quantitatively to do the Claisen condensation.