I'm not sure that HCR really affects anything other than possibly the overall difficulty of playing. Fatigue, Movement Restrictions based on armor, Hunger, Thirst, Damage from Extreme Weather, etc... , all make the play more difficult, but really have little impact on how you'd build creatures. I.e., it should have little impact on CR.
What will have a greater impact I think is the Economy and XP.
If supplies (especially healing and other restoratives) cost too much, adventuring becomes more of a burden than it'll ever be worth, especially in a HCR Module. Since HCR Modules are also generally "Low Magic", using the default creatures as is or as templates for tougher scaled versions is good way to start. Most of the Bioware Blueprints do a pretty decent job of following the D&D 3.0/3.5 Rules and Abilities.
