Hello Fraenk,
When I first got Ubuntu-Studio, it came with PD installed by default in a package named puredata. This is just the core of PD. I installed PD-extended without removing puredata and it worked with no noticeable problems.
However, the packages of PD-extended will not let you have both vanilla and extended installed at the same time if both done through synaptic. This is because apparently there are conflicts which I have personally not experienced since when I was running them both, I wasn't using PD much anyway.
You can try for yourself and see. If you NEED both versions for some reason (highly unlikely, I just did it cause I couldn't be bothered to look into it at that point), go for it and let us know what happened. If you NEED a STABLE version, just pick one of the two. They both are the same core, but PD-extended gives you a whole bunch of extra things such as libraries and externals and so on, already compiled, in the same package.
If you meant installing PD vanilla 0.41 and PD-extended 0.40.3, that's a different story, and the short answer is that it depends on how you compile it, otherwise you just stick to what the packages give you.
Take care,
Ilias