Wow that was quick :)
Here's a test map in the Quake3 BP format:
https://dl.dropboxusercontent.com/u/61424391/Quake%20Stuff/testq1q3.map
I compiled it with your new build and it seems to work fine, cheers!
So, here's how you set up NetRadiant to use the BP format:
Edit the q1.game file located somewhere like here:
"C:/NetRadiant/netradiant-custom/netradiant-custom-20160911/games/q1.game"
All you have to do is set brushtypes="quake3" and maptypes="mapq3".
Then in the editor, go to preferences->settings->brush and make sure the "brush primitives" checkbox is turned on.
Restart the editor. Now, when you are in quake 1 mode in NetRadiant, you will be reading and writing maps in the Quake3 BP format. Everything else is still Quake 1 style - wad textures work fine and all that.
I still need to pester the NetRadiant guy a bit more though. In the test map, I have included a crude terrain ceiling to illustrate the main problem with the editor's handling of the BP map format - which is ironic considering the format was created for Radiant in the first place...
When in BP mode there currently seems to be no way of telling a face to use the old axial projection - it's face projection all the time. Face projection is great to avoid the weird skewed textures on certain angled surfaces that you'd get in quake's original map format, but for stuff like gentle terrain you would almost always want axial projection to get seamless texturing.
The terrain in the map looks terrible because of this. But yeah I just need to pester the guy maintaining NetRadiant to add the ability to choose face or axial projection on a surface.
A little bonus thing you could do that is not important, but might be worth doing, would be to read Quake3's "detail" flag on brushes, as an alternative to using func_detail - this might come in handy for people who want to try converting existing Quake 3 maps over to Quake.