You say “ADS-B mlat” but FWIW we don’t do mlat on ADS-B messages. (I mean, you could - but given they already contain a position it’s not very useful). They’re used for synchronization only.
I have posted at length about the details of how the mlat system works in the past so I’m not going to go into it again (I’m sure google will find it, or look at mlat-server on github) but the short version is that position messages from ADS-B equipped aircraft are used as a common reference to synchronize the free-running sample clocks. Typical precision is around 0.5us. Then we use the synchronized clocks to do TDOA multilateration on non-ADS-B messages. The system time of the Pi is irrelevant and is not used.