You're going to love that thing. Yes they do have a personality. Just my imagination but I wonder if the original Japanese Yanmar tractor owners felt the tractor was a sentient member of their family like the water buffalo that their first tractor superceded.
That is the ordinary intake manifold/valve cover, and the undisturbed black paint there further supports that it is a low-hour engine. The air cleaner mount is unpainted, and the hose clamps on that crossover tube toward the air cleaner don't match the oem clamp right at the manifold. I conclude that whoever mounted the snow blower or whatever it was, extended the original U-shape of that intake hose and modified the air cleaner mounting to avoid interference with some new hardware on the left side of the engine. So it's not a Frankensteinmar assembled out of unrelated parts, just a rational modification to mount some third-party equipment.
Mismatched engine serial # and the non-original bolts between engine and bellhousing suggest a replacement identical engine. (Check that those bolts are tight!) The addition of an oil pressure gauge might suggest some catastrophic end to the first engine, but I don't recall ever reading here of such an event on a Yanmar.
'Turf' tires on a 4wd might indicate this was bought new for primarily snow removal, with tire chains. (This seems to work better than ag tires for snow). Do the tires show scuffs indicating chains? And I don't see the rust that is common from clearing salted roads for 30+ years, indicating excellent maintenance or non-urban use.
Do you see any remnants of hydraulics? That mount by the throttle and the adjacent wear on the fender suggest a hydraulic control was mounted there.