"Alter Ego" is no problem, because there never was any rule about beaming out
of a shielded ship. Indeed, the very first episode to feature any beaming rules at all, TOS "A Taste of Armageddon", featured a beam-out through shields while supposedly also telling us that Scotty couldn't beam Kirk in despite knowing his location.
Of course, this is nicely analogous with the ability to fire phasers out through shields while being protected from incoming fire.
It's "Maneuvers" that first features a beam-in under combat conditions. But since our heroes are fighting just the Kazon, perhaps they feel they can drop their shields for a while?
As for "Rise", Janeway indicates they can't
beam Neelix, Tuvok and pals up while the battle is raging, not trivially anyway ("We're a little busy"). But they can probably put the battle on hold for a while, as the enemy isn't after them as much as he is after the planet below. Perhaps Janeway just sacrificed a few Nezu cities?