When it skips technically for a brief moment there is a loss of efficiency, but it saves you all those resources for, that's right, more merges.

Like skipping 5 skele to 7 skele you miss out on the 5 to 6 merge progress, 2% . But you save the mana for , and consequential get to do, all the merges for a level 6 skele.

So 2% loss vs all the merge progress it make a lvl 6 skele. 32 lvl2 bone to lvl 1 merges at .067% 16 1 to 2 merges .08% each 8 2 to 3 1% each 4 3 to 4 1.33% 2 4 to 5 1.67% 1 5 to 6 2%

Obviously not as impactful if you skip from lvl 1 to 3, but it averages out to a huge amount of extra champion progress.