Does that piece exist on the PML under a different category, like a misc woodwind trio, with that instrumentation?

In a woodwind quartet you can choose any option that's given in the score, eg many quartets have the 2nd part as either flute 2 or oboe. Some brass ensembles have parts that could be trombone or baritone. You can make whatever choice of instruments you need in those cases. But in this case, a flute trio is no longer a flute trio if it includes a clarinet.