I use PCB Stackup to generate SVGs from the gerber files.
The svgs get converted (on the fly) to rasterised images in the browser. I build a model in three.js where I "punch out"/drill holes in the 3d model based on the transparent areas of the rasterised image. I was surprised of the result myself.
The arduino pro-mini clones have a couple of variants, where some of the pins are located differently.. the FTDI header is not included in the footprint above, and is on the left hand side of the footprint. With your particular pcb variant, the 3 pins on the right hand side (27, 28 and 29) is placed differently, but are still available on the footprint, at the correct places.
So yes, the footprint can be used for your variant as well..