Unfortunately you'll never get more than ~64k clipnodes from Q1 BSP as clipnode numbers as stored as 16-bit short integers in the BSP file itself. The format also needs negative numbers to be stored, so there is a further restriction that the highest positive clipnode number minus the lowest negative can't exceed ~64k.
This is a Q1 BSP format limitation, nothing really to do with the engine you're using. There are loads others (vertexes is particularly troublesome).
I'm actually surprised that more engines haven't gone down the high capacity route; I would have thought that it should be reasonably common by now.
FTE would probably run it too, but then again I have a feeling that FTE would probably run Pong maps if you tried.
