The main issuees with a DSLR and manual focusing is that there are 3 different optical paths, the sensor, the AF sensor, and the focus screen, ideally they should be an identical distance from the lens including the reflections off the mirrors(main and sub).
In reality, since AF has become so dominant the viewfinder has been mostly transformed into a framing system from a focus & framing system due to cost savings, why make the viewfinder super accurate when 95% of users will use AF only, 4% may use both and maybe 1% uses manual only vs 100% manual use back in the manual only days.
So accuracy was the first casualty, then the focus screen texture was altered to increase brightness at the expense of DOF representation in the viewfinder, so you don't actually see the actual DOF of the lens, only an approximation.
I owned the 30D, 40D, and 1DIII before moving to mirrorless(NEX-7 & A7r), I did little manual focusing with the 30 & 40D, I did a lot of manual focusing with the 1DIII with various focus screens, while manual focusing was possible, it wasn't ideal nailing the plane of focus was near impossible if the focus screen wasn't calibrated to the sensor(optical path length), you could buy shims for the 1D series focus screen to adjust the path length(which should have been done at the factory, but that costs $).
When I jumped to mirrorless, it was a whole different experience, the plane of focus and DOF in the file was always exactly the same as what I saw in the EVF(WYSIWYG), there was no trial and error, I didn't have to check my shots to see if I missed focus , I could usually tell if I nailed it or missed it, and I could see the actual captured DOF before I tripped the shutter.
For example if I wanted the plane of focus on a flowers stamen, I could generally get it quite close with the DSLR, but with the mirrorless, I could choose to place the plane of focus on the front or rear half of the stamen, or the very tip if I choose to, then add as much DOF to get the effect I wanted, it was a completely different experience I wasn't expecting, EVF was the future, and I was living it.
Focus confirmation wasn't really talked about all that much when I started shooting manual lenses, so I already bought a bunch of non chipped adapters and I didn't see any advantage in going back to relying on the AF sensor to nail the plane of focus when I had moved to manual focus because I couldn't nail it with AF in the first place, although AF micro adjustment did help immensely with AF accuracy I still couldn't nail focus like I wanted with all subjects, low contrast subjects remained near impossible with AF.