Hi Gus, if you install the WikiTree Sourcer extension it solves this problem for you like this: In the options you set which Ancestry domain you wish to use. Then you can right-click on any Ancestry link and use the "Sourcer: Open link in in new tab" and it will open it at your prefered Ancestry domain. This is demoed in the help video at time 14:57 in the "context menu" section.
I suggested a long time ago on G2G that the WikiTree site could solve this problem for users by having a similar option on the WikiTree Settings page and, when it displays a profile or FSP page automatically point the links to that location. I didn't get much support for that idea though.
Now that we have the new(ish) WikiTree Browser Extension this seems like something that it would be useful for it to do automatically as an option. [EDIT: This is actually already implemented - see comment below]
To answer your specific question: I would not put two different record links in the citation. As to which one to use, it doesn't matter if you use a feature like I described above, but is not really obvious which is "best" to use - the one that works for you or the one that works for the most people likely to look at the profile.