My idea
Make a script before calling pacman to compare obextra/ and extra/ repos for their qt5-base version. I remembered that pacman had those things called hooks and read into it. It's exactly what I was looking for. I'd like to publish this here on the forums for others to add to their system if they wanted to. I actually think this concept deserves some credit for the pacman devs.

So after reading the manual page it was pretty simple to build my own hook. There's just one downside. The actual "exec" field is quite a sucker to get right because of how whitespace and quotes are escaped.

[Trigger]
Operation = Upgrade
Operation = Install
Type = Package
Target = qt5-*

[Action]
Description = A version mismatch was found between upstream Arch and Obarun qt5-base! Pl>
When = PreTransaction
Depends = qt5-base
Exec = diff <(pacman -Sl obextra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}') <(pacman -Sl extra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}')
AbortOnFail

The idea is simple: Compare the version of extra/qt5-base and that of obextra/qt5-base (without the distro unique bit) whenever any Qt5 package wants to install or update.
You can run the above commands individually to see each repos version (and ONLY that!):

pacman -Sl obextra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}'
pacman -Sl extra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}'

By comparing those two you will get either nothing printed (diff exited 0) or a diff printed (exited not-zero).

diff <(pacman -Sl obextra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}') <(pacman -Sl extra | grep qt5-base | awk -F'base ' '{print substr($2,0,6)}')

You might change the substr() in one awk of this example—at times when both match—to still see the not-zero result.
This is exactly what I need for the "AbortOnFail" option.

I need help with the exec line [SOLVED]

I just can't get it right. First off the hook exec should usually use full paths or else it will throw an error of "call to execv failed (No such file or directory)". You can see this behavior by comparing the behavior of Exec = false and Exec = /usr/bin/false
Both will AbortOnFail. In the latter the program executed well but returned not-zero, the former executed wrong and returned not-zero but because of the execv error, not the program itself.

The man page says:

ALPM-HOOKS(5) wrote Values containing whitespace should be enclosed in quotes.

I have tried several ways of enclosing my command in quotes and also giving full paths for each piped program but to no avail. If I double quote the whole command the execv error will show. If I double quote the process substitutions in different ways I get a diff error of (No such file or directory) but no execv error.
This is easy to set up and test but difficult (at least for me) to get right.

Anybody firm with execv and quotes...?
Also there may be other ways to achieve this comparison. It's just what I have come up with after a bit of tinkering.

WIP/Edit:
At least I found a native way to only show the version of a package (still need to cut the distro bit)

diff <(pacman -S --print-format %v extra/qt5-base | head -c-2) <(pacman -S --print-format %v obextra/qt5-base | head -c-2)

I just found out how exec works here and found a solution. I'm now fiddling with the output. Once I'm happy with that I'll post my hook.