There are definitely times when Bard is preferred. Hot Foot, like you said (although see note below), and Raid Boss 2 in particular come to mind. I also prefer Barding on Raid Boss 3 over Musket due to group healing.
However, the two issues for me are
1: Encore, which we agree on needing an overhaul
2: Bard’s healing just being hopelessly outdone by Musketeer. With my numbers being pulled from a +5 Musket vs +6 Bard Mallets, Musket can get 3.5x the healing of Bard easily. Just Renew (which you can bounce to entire party) or the Turret alone outdoes the Bard heals per second, and considering that Musket also gets Shield Orb, Lifewell, and a bouncing Cure Wounds, the numbers are heavily skewed.
I do want to point out that on Hotfoot, two of our Musketeers in Elysium can deal with it just as easily as me Barding. I don’t know how they do it, but Hotfoot isn’t too much an issue there. I still prefer to Bard though, and when Golden Egg comes back, I still prefer to Bard on that!