This is one of the requirement not to enter the PDF links manually. Do you know who adds .htm to PDF? Can we customize this behavior?. I am sure Lot of people might have faced this before, and what is the recommendation.
i tried to validate in AEM6.1 geometrixx page properties - advanced tab - Login Page, but i did not see the behaviour which you have specified above, need to check in AEM 6.2 though. Can you also check in geometrixx from your end and make sure that if behaviour is same there as well?