You also need to consider the context of the SRM. Are fastener subsitutions per the SRM acceptable when reinstalling or replacing heavy structure? Probably not when you consider hole/fastener fit and clamp-up.
However, if you have a repair which calls for the use of Hi-Loks, such as a skin patch or stringer splice, and you can't get the collars on, by all means, use the nuts.
Hi Shear may be the manufacturer of the fastener "system," but the Type Certificate Holder determines what is acceptable to maintain their product in an airworthy condition. On the other hand, I don't think you'll get Boeing or Airbus to sign off on replacing an engine mount with nuts instead of collars.