I'd like to point out that, regarding Alertness, it almost necessarily has to be an intentional choice on TB's part to have it give Perception rather than the Alertness skill... unless the Perception stat was originally called Alertness, or something (perhaps someone who was around for the very, very early versions of the game could confirm).
There's a high chance that Healing works the same way - that it was an intentional override of the regular behaviour.
So I suspect that having Alertness and Healing be unavailable by wish was an intentional decision on the part of TB.
Healing can already be obtained early in the game from Jharod or the Mad Doctor (or whatever he's called), if you choose the Carpenter quest. Perhaps if a similar decision arose later in the game, in which one quest (or one way to finish a quest) allows you to obtain Alertness, were implemented, it would address this issue. Here's a possibility that comes to mind:
Right now, if one completes the Arena 20th battle quest, one can get the Golden Gladius, which you can give to Bart in exchange for training in Backstabbing, Tactics, and Two Weapon Combat. Of these, Tactics is perhaps the most significant skill, as it improves the effects of changing tactics. What if there were a different NPC, somewhere, who would also accept the Golden Gladius, in exchange for, say, Alertness, Dodge, and Food Preservation? Why those three? Because I see them as somewhat equivalent in value, and currently unavailable from an NPC. This leaves the player with a choice of which skillset is of greater value.
And since Bart also gives weapons training for it, I'd also perhaps consider having the new NPC give something equivalent to that. But since this RFE is about skills, I won't go into that.