Well, the basic problem is that 'cover' isn't well-defined at all, outside of the two situations... one, Keeping Hidden, and two, "To determine if a target...". You're not his target (remember that "target" has a specific game meaning) for anything; you're not using Stealth normally. So the cover rules, if narrowly construed, actually say nothing about the situation.
Which leaves it up to the DM to quite legitimately decide which is closer to the usage here. And IMO the fact that it calls for a Stealth roll makes it much closer to the Stealth situation than the targeting one. So... YMMV, but in my opinion it isn't even a house rule. It's a rules call on an unclear situation. Pending errata, the narrowly-construed RAW appears to say nothing about it at all. So it's up to the DM, even in Living Forgotten Realms.
Sure, give him a chance to retrain Black Arrow if he doesn't like it. But IMO the feat is still easily the best of the Style feats and well worth its weight. Betcha the player will feel so as well.