Well he can’t teleport or duplicate himself so he’s either doing one or the other. And if he’s in your base he’s not in lane, so you should be and you should be winning unless you’re being outplayed or the enemy composition is better, in either scenario Pendles being in your base has zero impact on the outcome of the match.
And when you do you can deal with him accordingly. If he takes your shards it’s either because he was already there or because you were too slow, and if he takes your thrall it’s because nobody on your team went for it in which case it’s fair game, he’s far from the only character who can infiltrate your base to steal shards/thralls.
Again, if you’re losing it’s less to do with him and more to do with the rest of his team outplaying yours because he has no presence in mid. People keep blaming one character or another on being too influential and winning matches without first considering player skill or team composition as factors, Pendles is not a character who can do this alone because he’s usually not in lane which is where most Incursion matches are won or lost.
No, that’s not a problem, punishing a character for doing what it’s supposed to be able to do would be a problem. That’s like saying you should be able to punish Kleese for setting up a rift network.
Her ult shouldn’t hit any stealth characters yet it does.