Let me try to answer

 2. Why is the version in Kali outdated, despite the package being available in Kali from Debian upstream?

kali-rolling is based on Debian Testing. The version in testing is 1.4.50+ds1-1 that's why we have this version in Kali.
The version 2.0.19+ds1-1 in only in Debian Experimental (https://tracker.debian.org/pkg/sqlalchemy)

1. Why is there a version discrepancy between the changelogs? Has Kali re-packaged sqlalchemy?

The version in Debian experimental has been uploaded a long time ago, the new upstream release 1.4.50 didn't exist. It has been released after (upstream maintenance).
That's why the debian/changelog does not mention the version 1.4.50.
The maintainer uploaded it in experimental because it's used by a lot of packages and an update will probably break some of them.

3. Since netexec requires python3-sqlalchemy version 2.0.4 or higher, is there any way of upgrading this package to the current one from Debian?

We are dependent on the Debian Python Team: If we import the new version in Kali, we will probably break a lot of packages and we don't have the resources to check and fix them all in Kali.
FTR the Debian Python Team is working on the Python 3.12 migration, and the version 1.4 is broken with Python 3.12 so maybe they will work on the update of sqlalchemy quickly.

We have other updates / packages blocked by this old version of sqlalchemy. I'm not sure if we can find a work around while waiting for the update on the Debian side.

Would you like me to raise a bug ticket with Debian to get the Debian Python Team to see if they can make this happen? If not, I will speak with the NetExec devs and see if they can lower their sqlalchemy version to what Kali has for the time being.

FYI
There is already a bug asking for the update: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1030164

And the last message about the update on the mailing list is here: https://lists.debian.org/debian-python/2024/02/msg00043.html

Ah great, thanks for sharing that Sophie.

Thanks for the insight as well - I totally overlooked the experimental tag.

You can close the ticket if you'd like :)