any real down side to running the 128meg card verses the 256?
Not really. You aren't likely to need that much VRAM without Warp3D. Even then you aren't going to run high enough resolutions to run out of VRAM, even with Warp3D. If you ever think you might want to install a PPC PCI card you want the Video Card to use less of the 512MB of Mediator memory space for the PPC memory space. So 256MB of VRAM means you can only have a maximum of 256MB on the PPC card. At least this is how I understand it works.
also, from what i can see, there are no warp 3d drivers for the radeon 9250 on OS3.x. is this right?
There are some youtube videos that suggest someone is working on this. But no not yet.
also seems you NEED to have a graphics card on the PCI bus to supply some local ram to the PCI side for, say, the NIC and Soundcard to be able to work?
Yes, but not a 10MB NIC.
I have an A4000Di mediator (circa 2002). I'm pretty sure this definitely 5volt only? i tried to buzz the 3.3volt pins on the board and got nothing. I'm pretty sure but is there anything else more obvious like a label i can look for to confirm?
Yes, if it's from 2002. The A4000 3.3V Mediators only came out in the last 6 years and they have a Black PCB. Except the A1200 Mediators they have had 3.3V support via ATX power supply for a long time.
The unofficial mediator guide is worth reading.
https://mediators.github.io/