Index dive/sampling row count very inaccurate in MySQL
Yes, the samples are inaccurate.  A factor of 2 is actually somewhat common.

It could be that the "random" probe is not very random, and may repeat some pages.

OPTIMIZE TABLE, which is generally useless, would rearrange the data, probably enough to change the statistics.

Consider writing a bug report at bugs.mysql.com .

A side comment:  A table with 3 unique indexes is extremely rare; it usually indicates a flaw in the schema design.  Perhaps nepotism is not allowed in the company?