I would agree with you that something similar to metric would eventually arise, but I would consider duodecimal to make more sense than decimal, as 12 is a superior highly composite number and the terminating representation is much shorter for more commonly used fractions (e.g. 1⁄4 would be represented as 0.3, 1⁄3 as 0.4, 1⁄2 as 0.6, etc). I would also argue that groupings in powers of 12² make more sense than 10³.
I would also argue that it would make more sense for measurements to be based on natural units (such as Planck length) for all the basic measurements (second, metre, kilogram, ampere, kelvin, mole, and candela), such that the anthropic unit (the one you’d most commonly refer to without prefixes) would be some multiple of 12 away from the natural unit.