Each of the Consul and Nevis seems to hurt a particular, different location in my feet, which I know is normal and part of a shoe breaking in
No, it is not normal for shoes to cause you pain as they "break in." Typically, properly fitted shoes are comfortable right from the start. If they cause you pain at the start, it's quite possible they'll always cause you pain.
Moreover, you say you bought the shoes in question months ago. And it sounds like you've worn them multiple times since then, for most of the day each time. If they haven't broken in by now, don't count on them breaking in.
Maybe the shoes just aren't a good match to your feet. This isn't an uncommon situation, particularly if your feet are, as indicated, "fleshy." It doesn't mean there's "a glitch with your feet." Just that not all shoes are a good match for all feet. Could be that the shape of their last, or some other aspect of their design and construction, just don't go well with your feet.
Or maybe you purchased the wrong size - and did you pay attention to width, as well as length? Many men have no idea what width shoes they should wear, and blithely assume their feet are medium width. Lots of these men are wrong. For that matter, many men don't really know what size (non-width) shoes their feet are - they just figure that since they were a size 10 when their feet "stopped growing" in 11th grade, that they're still a size 10, even though high school was 20 years ago.
Often, sneakers and casual footwear are less "fit critical" than are dress shoes, when it comes to proper size. (No, not always. I devote considerable effort to getting the best possible fit from my running shoes, for example. But often.) You can maybe get away with the size being slightly off when it comes to your Nikes. But with dress shoes, it's often more important to get the size exactly right. You indicate that these were your first ever "real" shoes. So I bring up this point.
bengal-stripe is correct about feet changing over the course of a day. It's very common for feet to swell considerably between the time you get up in the morning, and the time you get home in the evening. This is one reason why it's often preferable to shop for shoes at the end of the day, when your feet are at their size maximum, and not early in the day, when they're at their smallest. (Other factors - time of year, weight, fluid retention, etc., can also impact foot size. But time of day is perhaps the most obvious such influence.)