Haven't tried it myself. The manual doesn't say anything about rescan (Ctrl-F4) being imgmount only.
Will the game accept it if you mount the second folder as another letter?

I'm not sure. It's difficult to tell without a savegame before the change of the disc. I tried inverting the order of the mount:
mount d "CD2_DIR" -t cdrom
mount e "CD1_DIR" -t cdrom
and it starts, but of course, that is not certain. It might just ask for cd1 in drive e later.

But i can test if mount changes cd with ctrl + f4 in the shell. I don't know why i didn't think of it.
Edit: it doesn't. Damn.

Yes it does, as long as you mount the same drive and just change the physical CDs in your tray or similar loader thingie, I just tested it
mount x x:\ -t cdrom
I changed the CD and pressed ctrl-f4
and lo...it does change
The problem might be that the game you're trying to play (unlisted, BTW) is looking for a specific label on the CD...
Not to sound like I'm yelling but...space is really cheap these days, so...why not make some nice images?
On SCUMMVM: most games that use CDs in SCUMMVM can have their biggest data (the audio, usually, strip a divx video of audio and be amazed) compressed in some way so it's not that big an issue, really, just get the scummvm tools, a copy of the lame codec and compress your audio away!
Legend of Kyrandia 3 ~600 mb after making an iso image, after compressing with SCUMMVM tools: ~256 mb (in my case)
So, it's not really a problem, though I'm assuming you can compress the data, as no game was listed and not all of them can be processed by SCUMMVM tools.

I'm not using physical cd's. That's the whole point. And i told why i'm not using images.
Besides why not make mount and img mount as similar as possible? Consider this a RFE.

As for the two tries i mentioned (multiple drives with different root folders and trying to use multiple folders in a drive like in imgmount), neither works (and i am using read only dirs).

As to why not make mount and imgmount as similar as possible, I don't know, ask the developers...or...better yet, write your own patch 😁
As for not using physical CDs well...
This wasn't all that clear for me in that respect:

To change a "cd" drive. Before you yell at me to use imgmount, the reason i'm trying this is that scummvm doesn't work with imag […]
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To change a "cd" drive. Before you yell at me to use imgmount, the reason i'm trying this is that scummvm doesn't work with image files and i'd like to play both versions of the game without duplicated files. So i'm planing either to mount 2 subdirs as different drives (if the game allows it when changing cd) or mount in the same dir and change the same as imgmount (if dosbox allows it).
[...]
mount d "CD2_DIR" -t cdrom
mount e "CD1_DIR" -t cdrom

BUT if you want to avoid duplicates, why not use physical CDs??
Ok, here's another thought...why not make your two folders just one?
Most games (as SCUMMV proves, since you're using it, but it amazes me how it works with two data dirs for the same game...now there's something I thought was impossible) have a set of common data on both cds and with any luck, the game will try to look for an specific file on the second cd when the change is requested and happily play along as you press enter, click ok, or whatever you need to do to acknowledge the CD change.
Other than that...I'm out of ideas, except "we can't always get what we want"

It works for broken sword quite simply because its common NAMED files (the speech & audio) can be made to reside in different directories by some judicious config file editing. This + the symlinks allows it to work both in dosbox and scummvm. Unfortunately dosbox has a bug in broken sword or vice-versa.

With discworld this is impossible without some heavy exe editing. The file names are hardcoded.

I guess the choice is between the original game and scummvm now. As i'm not about to create a "scummvm games" folder to add to my "dos games" and "wine games" folder, the decision is obvious. No scummvm for you discworld 2.