I don't understand the 90 vs 100 skill thing, in terms of something being possible in the 90's, but not 100. How does having those 10 extra skill levels act as a detriment towards HQs? That doesn't make a lick of sense.
This isn't always the case. However, if you are trying to HQ something with rather high subcraft requirements, then yes, having 100 skill can be a detriment.
The example given here were Hellfires:
Smithing 89, Goldsmithing 54, Woodworking ?
Let's just work on Smithing and Goldsmithing for now. If you have maxed out Smithing @ 100, you are at the 11-tier for HQ. However, the max GS you can have is 60 + shades + adv imagery = 64 which is 1 level short of reaching 11-tier. As it seems that you need to satisfy tier requirements on all the craftskills, you won't be able to HQ this much.
On the other hand, at Smithing 99, you can have Goldsmithing up at 61. Thus, with your Smither's Apron, Shaded Specs and Goldsmithing Advanced Imagery, your Smithing is 99+1 (=100), while Goldsmithing is 61+3+1 (=65). You are now at the 11-tier on both Smithing and Goldsmithing and can HQ Hellfires more.