My last option is to use a base that has a milled reference edge on cast iron or Al since it is more expensive than a granite surface plate.

Obtaining a surface finish down to near 1 micron on cast iron or Alu will be more expensive and is not easily readily available off the shelves at low prices like granite surface plate.

On Amazon, Granite Surface Plate 12" x 18" x 3" A Grade with a surface finish of 0.00005" (1.27 microns) for $148 with free shipping:

https://www.amazon.com/Granite-Surface-Plate-18-Grade/dp/B006JYKIE4?th=1

This is really a steal of this price for the project needs. Highly doubt cast or alu with similar specifications around that price.

One thing I can not figure out, why does the linear rails need a milled reference edge to begin with? Is it to make it simpler to install or is it to provide more rigidity on the rails due to an uneventful crash, or maybe both?

I have seen short limited documentation of installing rails using without a milled reference edge, but it requires a precision granite square or precision granite straight edge which I do not know how to place and align it to aid the installation of the rails.

I think it will be more economical to bore/drill holes into the granite surface plate to bolt the linear rails, would like to get some advice on how to do it and how to bolt it while keeping accuracies close to 10 microns.

Thanks for the PDF, I actually downloaded this 1 week ago, it's not really helpful and doesn't discuss much. It's presented in such way that only experienced can comprehend. I just wish they added much more details. I also saw videos from NSK on youtube of installation rails, it too not much of details and specifics on way of doing things.