Not easy to do this any differently. The “better” way to do it would be to have separate baselines for each hole that would take into account, e.g., placement of hazards, but this really isn’t feasible. The second answer is that you might be losing 0.25, but that is better than taking on the hazard and, on average losing, more than 0.25. A “correct” strategy will have a better average strokes gained, but, unfortunately it can appear as a negative number.
Here’s another extreme example. Suppose a player duffs shots from 20-40 yards. So this player lays up to 70 yards and has a negative stokes gained for the approach shot. But for this player it’s still a better strategy than laying up closer to the hole (with would improve his approach shot strokes gained) and then experiencing the more negative strokes gained from 20-40 yards. For this player, I’d hope the negative strokes gained from 20-40 would lead the player to improve that part of his game and it would have the secondary benefit of improving his approach shot strokes gained.