In terms of sheer image quality, it's highly unlikely you'll find huge and significant differences between an APS-C sensor mirrorless camera and an APS-C dSLR camera. A micro four-thirds camera with its smaller sensor might have an advantage in getting you more depth of field for macro photography.

However, specifically for specializing in macro photography, a dSLR might be a better choice simply because you'll have a few more choices of possible macro lenses you can use, and quite a bit more freedom on choice of flash gear. Flash can become important with macro photography because depth of field becomes very small, and most shooters counteract that with smaller aperture settings, but that cuts down on the light. And macro photography also magnifies camera shake, so flash and tripods are often typical gear for a dedicated macro shooter. And there are other possible tools like tilt-shift lenses, bellows, lens reversal rings, cable releases, and wireless shutter remotes, which are easier to source for dSLR mounts (since they're older and have been popular for much longer, the 3rd party support is greater). Doesn't mean you can't find them for Fuji X, but a few of these may be much harder to find or nonexistent.

In the Fuji X-mount system, there's only a single macro lens: the 60mm f/2.4 Macro. There are also a Zeiss 50mm macro, and a Samyang 100mm macro (basically the same as their dSLR version of the lens), but the selection is relatively limited.

In the Canon EOS mount, however, with an entry-level dSLR body, you'd have a choice of the old discontinued EF 100mm f/2.8 USM Macro, the EF-S 60mm f/2.8 USM Macro, the 100mm f/2.8L IS USM Macro, and the oddball expensive MP-E 65mm f/2.8 1-5x Macro. Not to mention the Tamron 90mm f/2.8, Sigma's 105mm, 150mm, and 180mm macros, and Tokina's 100 f/2.8 Macro. And also the Zeiss 50mm macro, Zeiss 100mm macro, and Samyang 100mm macro.

And while you could possibly use the same lenses with an adapter, you'd lose autofocus and electronic communication with your camera, and you might not have any aperture control if the lens doesn't have an aperture ring on it.

If the 60mm f/2.8 suits your needs, however, then does it really matter? However, the focal length does determine the working distance which can have an effect depending on how shy your subject is and whether it crawls, hops, or flies away when humans loom over them. If you shoot mainly flowers, again, does it really matter?

Again, Canon has a wide variety of flash units, including two ring flashes and a TTL-capable wireless flash protocol that's full-featured, robust, and well-supported by 3rd party options. Fuji X, well... not so much. Fuji X doesn't (at the time of this writing) have a Fuji-branded flash that performs HSS. No ring flash option, and no TTL wireless flash protocol that 3rd parties can build on.

That's not to say you can't use an X-Pro1 and stay in the Fuji X camp. It's certainly simpler to use the gear you already own, the colors are amazing, the camera's viewfinder makes the experience of shooting one quite different from a dSLR. And it may take you quite a while to hit one of these gear limits I've mentioned (if you hit one at all). It's just a matter of how far you're prepared to go (and spend) on gear.