I haven't thought too much into it at this point, but I know I'll designate the course as Honors if it was provided by an outside provider. However, I can tell you that I have a family member who does the admissions at one of the "Big 12" schools in Texas and according to them, as a homeschool student the GPA is a -wash. So, it won't matter. Yes, they look at what courses our children take but the GPA doesn't really mean a lot...so giving weight to courses won't matter at this particular college. The big factor to them boils down to SAT/ACT scores and completing those required courses.
All this to say, that hasn't stopped me from making my children take Honors, AP and dual credit courses...and designating them on transcripts.