The main difference is that Freeview don't supply any boxes and don't charge a subsciption. If customers can't receive a service then the fault lies with their choice of manufacturer.
Sky supply theirs and charge subs. Nobody is going to continue paying for a service if they can't see many of the channels on the EPG. Consequently, Sky would either have to replace the box (free) or accept that some customers may leave.
Oh I see. That said, some people might be glad if their Sky digibox didn't have memory capacity to store all currently available channels, e.g. ...
Some people might be only too glad to see the box unable to store the shopping channels, holiday channels, religious channels (e.g. God TV) and foreign channels (e.g. Zee TV, Star, TVE International).
People without children might not mind the box not having sufficient memory to hold the kids' channels.
Parents with children in the house would only be too glad to see the box unable to store the adult channels like Television X, then they needn't fear their little-uns tuning into those. For example, say your three year old has learned how to switch from Nick Jr to CBeebies by tapping in the 3 digit number, he/she could just as readily switch to Television X / Playboy given the number.
I bet many people think that getting all the BBC One regions other than their correct local one is a waste of
EPG space, and wouldn't mind if their Sky digibox being unable to hold them all (as long as they could get just their own relevant one, e.g. BBC One West if you live in Bristol or Bath).