You posted two links to images of master cylinders and then asked,
This cylinder has some sort of rubber seals, whilst this one doesn't look to have them or they're a different color and hard to see. Both cylinders have the same OEM number. Actual question: Are these rubber seals swappable or can the mechanic just use some regular rubber shaped to fill those holes?
It's hard to know what from the photo you're referencing as "rubber seals." It sounds like you're indicating that you think these photos are showing "seals" and those are the specific parts you're worried about replacing.
Master cylinders do indeed have very important seals - the seal that seals the piston in the cylinder. You can't see that seal under normal use (or in either of your photos), but that seal is what lets the cylinder build pressure as the piston moves in the cylinder. Generally, it's possible to remove and replace the seal, although that means finding the correct part, and many master cylinder manufacturers don't sell seals separately - only whole intact units. Replacing that seal means ensuring that the piston and cylinder are in good shape, and it's often the case that if the unit's condition is bad enough that the seal is gone from old age or wear, the cylinder bore may be scratched or corroded as well.
The photos you posted do have some other "seal like" parts in them. The first photo has red plugs in the fittings where the brake lines would be attached to the cylinder. These plugs are temporary, to keep the cylinder from becoming contaminated while in storage. They're removed when the unit is installed in the vehicle. in this photo, there's also a rubber bushing on the bottom of a post sticking downwards from the plastic fluid reservoir - that's likely there as a bushing to fit that post into a mounting point in the vehicle. It's probably not replaceable separately.
Your second photo is taken with the fluid reservoir removed. The photo is looking down at the top of the unit, at the mounting fittings where the reservoir would normally be mounted. Those two fittings allow fluid to flow between the reservoir and the master cylinder. There are rubber bushings inside those fittings (it's usually a friction fit for the male fittings on the reservoir). Those bushings may be replaceable separately, and they may even come in a rebuild kit with the internal seal included.
The photos you've posted look like the Ate master cylinder used in some smaller Volvos and Fords maybe 10 - 15 years ago. I did a quick google search and didn't see a rebuild kit but you may have better luck spending some more time looking.