I've built a LOT of systems in mid tower cases over the last ten years (Longer really, but for more modern case designs we'll stick to those from the last ten years) and honestly this is the fan configuration I've used for them ALL, and I've never, not once, had any problem with installing fans in the rear-most top fan location due to the EPS 12v 4pin, 4+4 pin or 4+4+4 pin CPU power connectors. Your Meshify S2 case is actually even BIGGER than my Define S case, so you should have MORE room there than I do.
You may need to route that cable in through one of the small openings from the backside of the motherboard tray and then manually put a 90 degree bend in the cable by, well, bending it so that the wiring doesn't stick up any further than is necessary and then plugging it into the EPS socket along the top edge of the motherboard, but there is absolutely no reason why you should not be able to put a fan there. EVERY person with the Meshify 2, well, maybe not EVERY person, but I'd guess probably 90% of them, has to do that exact thing and nobody has any problems. If there were problems doing that, EVERY tech enthusiast in the world and every reviewer would be screaming at Fractal design about it being a design flaw, and they aren't, so it's not.
Consider, I have personally built a system in that exact case for a client, using a fan in the exact fan location we are talking about, that was a 140mm Fractal design fan (Model doesn't really make any difference. Yes, there are 15mm thick fans, but those are specialty items. Nearly ALL 140mm fans on the market are 25mm thick, so there is a standard across the board and really no room for variation), with a Thermalright Macho rev.C air cooler installed, and there was no problem plugging in the EPS 12v 4+4 CPU power connector.
Of note though is the fact that this probably HAS to be done with the CPU cooler OUT of the case, so that you have room to get in there and do what needs to be done including routing the cable in through one of the two grommeted cable management holes coming from the backside of the motherboard tray, as seen in the image below. You will STILL need to bend the wiring bundle down a little bit though probably, so that the bundle has a lower profile than the body of the fan, or tuck it up between the fan and the motherboard tray itself because there WILL be a small amount of room remaining there when the fan is properly mounted. It will definitely fit, no question, if you take the time to figure it out and do it right. There is plenty of room and this SHOULD be a non-issue. I'm not doubting that it feels like there is interference, or a lack of space, but I'd chalk this up to simply not being tremendously experienced with building and cable management moreso than because it actually doesn't fit.
If it couldn't fit, then the same problem would exist for pretty much ALL mid tower cases, and that just isn't "a thing".