Let there be meaning

[nablator]

Well, if you literally apply the cipher from my article to Voynichese, you don't need external props to count the distances. There are only three distances in my version of the cipher: roughly two characters wide (like kek), roughly four characters wide (keoek) and roughly six characters wide (keoyedk). They are quite unambiguous in practice. It gets much harder if you add the fourth distance, but three shouldn't be a problem.

You should define "roughly".

From your example:
The two k in key.qok are 6 chars apart, why kk2 and not kk3?
The two k in keedy.qok are 8 chars apart, why kk3 and not kk4?

If dots are not counted, then you will have 1,2,3 apart all at distance 1, is that right?

If there is a way to limit distances to something as low as 3, it would be in itself a very interesting result.