It seems weird that a system would eventually settle on just full stops and commas, yet not settle on where to put them. If your system is going to converge strongly on two symbols, finish the job!
Same reason why there are different date formats, weeks start on Sundays/Mondays (or Saturdays), long/short scale numbers, drives on left/right, different wall sockets and plugs, different train gauges, and of course metric/imperial.
It's a mix of tradition, conventions, inertia.
It just reflects the spoken language. And having the unused symbol then be the thousand separator is natural.