With flat film, the negative mask holds it flat. I've also taped the negative to the glass without problems. If the negatives are squirrelly, I'll wet mount them using Lumina fluid and scanning mylar.
I focus using live view zoomed all the way in. Focus is achieved by moving the whole lens, extension tube, cameras system up and down using a Velmex 4000 series unislide. (At 1:1, that's the best way to focus. At that magnification, changing lens to sensor plane distance changes magnification more than focus.)
So here are some comparisons.
First, we have a scan from the dslr scanner. The layers are from different lenses.https://dl.dropboxusercontent.com/u/...ergger_200.tif
This is a full-sized 8-bit Gamma 2.2 layered file. The sample area was the center of a 4x5" of Bergger 200 film developed in PMK. It was taped to the glass. With one lens, the exposure was 1/100th of a second, and with the other one it was 1/60th. I used the light source to roughly equalize the channels.
The files were brought into Lightroom 5, where I inverted them. I then used the curve feature to stretch each channel until it almost clipped, which should be pretty representative of actual use. Default Lightroom sharpening was applied to both. (Each could stand quite a bit more sharpening.)
After bringing the files into Photoshop, I converted to Grayscale 2.2 using the green channels, which showed a little more detail.
Second, we have a scan of the same area on my Cezanne:https://dl.dropboxusercontent.com/u/..._test-0109.tif
I scanned this version at 8000 spi and then down-sampled to roughly the size of the dslr scan in Photoshop using Bicubric sharper. No other sharpening was applied.