Mewtwo not getting Electro Ball might just be an oversight but I can at least see Deoxys getting Dark Pulse by the time it's actually available and the others getting their moves added to their levle up movepool where appropriate. iirc all the Johto Beasts got their other moves added in provided they were in the TR pool (ie Aura Sphere) so them also getting Extreme Speed & Sheer Cold and so on would make sense. And frankly Heatran should have already had Eruption.
I think that being able to make any old legend legal will mean that HA versions of the legends will be made available through the dens too, just so that they aren't (in certain cases!) left out from being the best they can be. The possibility of HA legends could also be enticing to keep grinding the mode until you get one, too.