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Restart your machine first, otherwise you will cheat using the disk cache ;-)
...and of course you need to enable "recompress" in cmpro's rebuilder... (which corresponds to 'rezip')
Would be interesting to see....I mean with turning on "rezip" you of course disabled the major speed optimization....since it doesn't copy full archives in that case

Whole process started exactly 16:00:00. 7:58 took scan rebuild process was ended exactly at 20:16:10.

Now let's see how it will take with use of clrmame.

ok...looks like other people also give some feedback:

a complete 253 (roms + chds) split sets to "mode: full" rebuild, "compress: zip", "sha: none", on one and the same HD without deletion of source files: 3441,69 seconds....which is 57 minutes...

...but "use links: hard" was used....so...a little bit of cheating :-) but still...remarkable

I pretty sure  a recursive commandline unzip -t on all archives afterwards would be faster ;-) but ok...

It's intentional - I'm not sure if source zip file is checked against any errors so I need everything rezipped. Anyway 46 % done and about 2 hours and 40 mins passed.

rezip...yikes...that of course unzips each file from each archive to temp and recompresses the files....why do you do that? If you want zip files in your destination, simply use "zip"....if something decompressed, something in a rar or 7z matches in the source it will be (unpacked) and repacked to zip....everything which is already zipped in the source can be copied without unpack/repacking....you're wasting time with rezip ;-)

Rebuilder reported 170398 unique roms. 23% and about 2 hours pass. I'm using rezip method but this probably does not matter since all roms are extracted from zip archives.

hmm...all mechanial ones (3 chds, ~15k sets), old cmpro (without chds): 210 seconds, new rebuilder (with chds): 109 seconds...
(split, no sha1, zip2zip, hd to (different) hd)

no problem...such things do happen..

I understand that CMP, unlike RV might want to duplicate roms shared between clones if there is no merge TAG present. but not honoring the filesize and CRC as described in the XML seems weird.. Where is it getting this from?

Easy answer: You're tring to scan a 253 collection with a MAME binary based on 239 (the window title of your screenshot shows it). Back then the hashes were different.

I've just noticed it after I made a split set. man, I feel dumb now. Must have grabbed an old mame version of my drive to create the profile. *hitting head against the wall*
Sorry about the rant, and wasting your time.