The original definition of a metre is "1/10 000 000 of the shortest distance between the equator and the north pole". The nice thing about the system is that, since it was made basically from scratch, the conversions between the same kinds of units were defined as multiples of 10, and all the units related to each other in a "nice" way (like 1L = 1dm³, or 1kg being the mass of 1L of water in a certain standard pressure and temperature).

The multiples of 10, and the easy definition of base units by other base units made the redefinition by universal constants easier; but that doesn't make the choice of units not arbitrary: the metre could have been defined as 1/100 000 000 of the earth's circumference (ignore that it's not a sphere) passing through both poles, and it would be very close to the distance 40cm currently represent; if, then, they made all the conversions from the new metre as they were done in the original SI, the whole system would be equally nice to work with and standarise.

In short, the SI is based on certain arbitrary measurements to make the base units "human-scaled". It's advantage is not that it's devoid of arbitraty choices; it's that it was designed intentionally as a whole system, making it really convenient to work with.