I just tried that and there are problems there too; specifically with the tnodes used for light.exe ray casting. You can kludge around it by running QBSP twice, once for the real BSP tree and once to include selected bmodels in the tree (by merging their brushes into the world during entity loading, same as is currently done for func_group in certain QBSPs), then mod Light to read from the second run for generating tnodes. It almost kinda works too, but generates some bad glitches in certain areas.
On the other hand it looks as though the QF tools actually do generate a valid Q1 BSP file so it may be viable to say "we're not gonna get it perfect, what's second best?" and accept a different .prt format (.pr2?) and mods to both QBSP and Vis.