I don't think you want to rename  the ID field, even if you find a way.
That's how SharePoint identifies the item (as opposed to its name or
anything else).
If you're creating a linked field in a list, you should be able to
select which field you want to display. Of course, this assumes the field
isn't hidden; which field are you trying to display instead?

Re SPD killing your "other functionality", I have found that SPD is VERY VERY
picky about what you do, and specifically the sequence in which you do things.
I know, it sounds bizzare, but it is my experience.

On the other hand, I have never found SPD to "kill" (disable) any
functionality that I build in the UI in the first place.

If I use SPD, then I have to convert  my list  UI to XSLT view  so that I can give
hyperlinking to ID (or any other field).
Also, with XSLT view I couldnt find way to display the Count or Sum of a column
values of list which was easy when using UI. (or do you have the trick to do
this?)

I also can not Hyperlink the Attachment icon to its Attachment file with XSLT
view.
Thats why I prefered to use UI.
But with UI I cant get the ID or other column  linked than title  column
Hope you got the problem.