The one will not conflict with the other. Our planned extension is compatible with every case that fits for N900. You might have a hard work ahead to extend the hole for USB receptacle, when the case is made from titanium or V2A or glass. The rest is a non-issue. Antennae of Neo900 will fail in a alu case just like the ones of N900

For the more expensive but smaller components: simply not available, the choice is like "use a modem module (height 2.1mm) for 150EUR" vs "use a small chipset (height 1mm) for 50EUR and get the cert and calib done for 500EUR per device, on a batch of 1000" - development not included. Since Nokia has own labs and own calibration tools at fab line and own modem chipset and builds batches of 100k rather than 0.5k, of course for them the chipset option is waaay cheaper, and thus no module fits into the original N900 mechanical design.
Even when you were willing to pay those additional 400EUR for the Neo900, we would need another 999 users also willing to pay 400EUR more just to get rid of the extension. I really would adore to go that direction, but I doubt it will fly.

/j