How do barometric altimetry systems compensate for nonstandard pressure lapse rates?
They don't.

Since all aircraft in an area are (or at least should be) having roughly the same error, the errors cancel out and there is no practical effect on vertical separation.

Falsely low readings result in more terrain or obstacle clearance than needed, so that's not a problem either.

Falsely high readings do potentially create a problem, but the minimum clearance is deliberately large to account for the accepted range of altimetry error plus some additional buffer. For example, it doesn't matter if you're 100ft lower than you think when you're still 900ft (rather than 1000ft) above any hazards.