From what little I know about the 2d barcodes, the individual dots need to be a minimum size to be scannable, and different versions of the barcode end up as different sizes as the result.
The fonts that are used may come in differing sizes (for example, the universal version of the ID Automation barcode font comes in 6 ttf files for 6 diff default heights/widths, each works best at 12pt). Each font can be scaled up/down to fit the space needed by changing the font height (pt size). The smallest of the fonts wouldn't scale to be particularly good when set to 72pt, but the largest does.
These same principles should apply to the QR code fonts as well (from what I can see, the ID Automation 2d fonts support multiple pt sizes).
You might need to try diff sizes of the font for different versions of the QR-Code, but you should be able to get them all to be relatively close to the same overall width/height even though the dot sizes differ. You just can't make the dot size so small that the scanners have problems with it.
That's what money is for.
Olan
Thanks again for the pointer!