And let me be more blunt since I tried to get around it. They aren't trading Baez. They are hoarding the bats that are at or about MLB ready. That includes Castro, Rizzo, Baez, Bryant and Soler. I doubt they are looking to trade Russell either, but I don't feel as certain about him as I do the other 3 prospects.
I'm not going to get in a debate on whether the will or not because it's fruitless. All I will say is you should consider why they are hoarding bats. It's because pitchers in the minors is notoriously unreliable and hard to predict. It's substantially easier to predict pitchers at the major league level or near there. Admittedly this is speculation on my part but it would be quite smart to let other teams suffer that attrition and use your more reliable hitting prospects to deal for pitching. The "cost" of doing this is actually even better than it may appear. Hypothetically, let's say they were to deal 3 hitting prospects for a top flight starter. It's not just about the cost of that pitcher but also the hidden cost you save by not having to trudge through pitchers in the minors to find that guy.
I frankly don't buy the bullshit they are trying to sell that there's room for everyone. Even if there were, playing someone like Baez/Russell/Castro in the OF is a huge waste of potential value. And even if they do move those players to that OF that's then cutting someone else out. Soler, Alcantara, McKinney, Schwarber and Almora are all already legitimate starter prospects in the OF in their own regard. So, trying to add another guy to that mix isn't going to work. Some of those guys probably will end up being disappointing but you're still talking about 6 players for 3 positions and that's prior to any FA dealings.
So, while I'm not going to say it's foregone that they will trade Baez, I think it's almost a guarantee they will trade someone in the next two years and if you're looking at this logically as to who they would trade would it be Baez a player they inherited from a previous regime and whom their current scouting director suggested wasn't on the Padres radar had the cubs passed on him in the draft or would it be Almora(their first draft pick), McKinney(player they chose in a recent trade), Schwarber(another top 5 pick from them), Soler(a player they signed), Russell(another player they chose in a recent trade) or Castro(who they went out of their way to assure after trading for Russell)? I suppose you could make this same argument for Alcantara as well but he's one of the few top of the order types they have and has much more utility.
Like I've said elsewhere, it's possible I'm reading too far into things but to suggest this isn't a compelling argument seems naive to me. Just as an example, consider what the previous Padre regime did upon coming to power. They took the now cubs regime's choice at 1B(Rizzo) and dealt him after acquiring Alonso who they got after trading away Latos. Kind of an eerily similar situation to Russell/Baez/Shark wouldn't you say?