This is actually a known flaw with chdman. The program does this with all cd images with multiple tracks separated into their own bin files. When it extracts the data, it keeps the tracks in the same file. To resolve this, you'll have to get a third party program to split the files. I've recently tested a python 3 script that seems to work perfectly.
I've gone as far as ripped one of my PSX games, confirmed it was redump identical, then using chdman, compressed and then decompressed the files, and using the script I'll link at the bottom of this post, was able to create identical track files that matched with MD5, SHA1, and SHA256 checksums to the original dump. I even used it to merge them back together, and the result was identical to the chdman extracted output.
https://github.com/putnam/binmerge