Do you have JACK1 or JACK2 installed? it could be that the builds of pd-extended and Ardour that you have require different versions, but they can’t be installed at the same time.
Also, where did you get your packages for pd-extended and ardour from?
It sounds like you are installing from a repo, gotta talk to your package maintainers about this, it has nothing to do with Ardour itself. The binary download from this site for instance removes nothing.
What version of Ubuntu are you running? If you include into like that, people may be in a position to give more detailed advice.
It’s possible that PD (or a package it depends on) clashes with ardour2 or one of its dependencies: indeed if your system says it will remove PD-extended whan you install Ardour2, than that’s what it will do.
You could always re-install puredata afterwards (which in turn will remove Ardour2)
There is bound to be a way of the two peacefully co-existing, but maybe not on the particular version of the distribution you have installed.