I have never bothered verifying anything I have downloaded against md5s, a better solution would be to just display what version you downloaded last, makes it heaps easier to check than to do md5 (or just make an optional download/update program)
I agree the setup should reflect the version number but that version number won't verify the integrity of the contents. Maybe not everyone wants to install everything they buy right away and as it stands you currently have to do that with the new setups and the lack of md5 posted to verify the contents. I'm honestly less inclined to buy stuff I'm not going to play right away now.
The point is - its effortless to do and could be automated - helps bandwidth challenged - saves money on bandwidth - saves time troubleshooting.
Just because you haven't used a technology doesn't make it not relevant. Source code repositories - server technologies - many aspects of computer science use a similar ideology to verify contents of delivery. CRC in the form of *.sfv files is another example that's been around forever - and still very relevant.
I could throw security in there as well as a good excuse.
Also since the games are DRM and/or "Fingerprint" absent, this is the perfect way to prove to the community that you have the same file as the next guy.