The Tektro R539s are medium reach brakes. Reach, in this case, is the distance that the pads can travel in their slots relative to some fixed point (probably the brake's pivot). Most performance road bikes with rim brakes have/had use standard or short reach, which is usually something like 39-49mm. The R539s have a reach, as you can see if you find the line in their specifications, of 47-57mm. Actually, you might not see it because not everyone knows about this parameter, and the Tektro specifications call it "dimension", which is spectacularly uninformative. And Shimano's specs for the R7000 calipers are only a little better. They say "Reach (mm): 51" - really, it's a range that contains 51mm, and based on prior knowledge I would infer that this is the maximum reach of the brake, but I'm honestly not 100% sure.
If your bike was specced with mid reach brakes, I would have recommended getting mid reach calipers, but these are a niche product. None of the big 3 make these anymore, although Shimano had an Ultegra-level (and possibly 105-level) mid reach brake at one point. There are indeed third party manufacturers like Tektro.
If you are sure about your measurement that the pads contact the rim correctly on one brake and you really need 2mm more travel on the other brake, then I would argue that it is OK to use a file to extend that slot by 2mm. Normally, we would not advise filing off metal parts like this. However, the brake arm is pretty thick aluminum in that area. You will void the manufacturer warranty, and I would assume that there's now a small but non-zero probability of some sort of stress riser causing a failure some time down the road. However, it should be safe within practical limits. I know I had this done on a rear Campagnolo Chorus caliper for my bike. That bike was custom and it was designed for short reach brakes, but it did push the limits because I asked for some clearance in case I wanted to run fenders. That caliper probably had at least 5 years of service with that modification before I sold it (with disclosure, mind you).
With the brake caliper in the other answer, there doesn't look like much spare metal at the end of the slot. On my R8000 brakes, I made a quick visual check (albeit without calipers), and it does look like there's enough metal for you to file downwards by 2mm safely. R8000 should be the same physical dimensions as R7000.
A linguistic note: in the bicycle industry, "reach" is commonly used to measure how far one part is from another part. Most cyclists think of frame sizing in terms of a key tube length (e.g. seat or top tube length) or an ordinal size (e.g. small, medium, large), but reach is used in this context to state how long a frame is in its horizontal dimension, measured from the center of the bottom bracket. Handlebars have reach figures as well, stating how far the drops are from a hypothetical centerline. Shift levers don't have reach measurements that are clearly defined and made public, but reach adjustment is a common feature whereby you can move the brake lever closer to the handlebar with an allen key. Reach obviously has the same physical dimensions as length. I guess the differentiating factor is that reach seems to be used in reference to a key reference point that's substantively important in its own right.
However, length and width do need similar reference points defined, e.g. are your handlebars 400mm from center to center, or 400mm from outside to outside? In real terms, there's about a 20mm difference in width just between those two measurement styles.