Have I talked about why this one doesn't work? Homing attack is notably bad at homing in on moving targets. It's startup is 23-34 depending on mashing, plus travel time. It's always slow enough for a human to react with shield every day of the week. So changing the move's startup by a bit doesn't make a real mixup. You either hold shield when you see it coming or...continue to hold shield. By mashing to perform it earlier, it goes from 12% damage to 5%. When hitting a target, endlag is 31, more than enough to punish out of shield with an aerial, especially if you blocked the weaker variety. If you collide with a solid surface such as the ground or a wall, endlag is 39, but you'll be able to perform double jump and Up B afterward, so there's a slight recovery mixup niche under a stage. But it's a totally nonviable attack otherwise. D tier is appropriate.
On a 2% launching hit. Knockback scaling depends on damage just as much as KBG. In practice, Peach's counter only keeps up with others or even exceeds them in knockback at high %s when countering low% attacks like jabs, multihit moves, etc. Fortunately, most recovery hitboxes fall in this category. So when you use Toad to edgeguard, you're getting results in line with Marth, sometimes even better. But for a direct comparison of a stronger move, countering Lucina's Fsmash from the default CPU position of Training Mode FD, Marth's counter will kill her about 40% sooner than Peach's. That's for a 15% damage move, and the differential continues to grow regarding even stronger moves.
There isn't anything exceptionally wrong with Toad, it just performs a bit differently. Counters get used most often as an edgeguarding tool, and Toad doesn't underperform for most of those scenarios. Its tier placement should reflect that, as D tier is still a collection of moves with critical flaws, even after you boot Falcon and maybe Ness or Ganon down.
Sorry, but much of that is false. Flame pillar doesn't have combos on its own, and Charge Blast's startup is 15 and endlag is 36 (I counted it, Kurogane could not find correct numbers). Furthermore, Charge blast takes even longer to reach full than Samus (144 to Samus' 136, making it the longest unless you count Donkey Kong's Giant Punch at 154). Factor in the lesser damage, knockback, and hitbox size, and it's a straight downgrade from Charge Shot. Gunner's non-combo, zoning moveset does it no favors for setups either.
That all having been said, B tier is sensible, since it sounds like Samus is moving to A, and a lot of C tier just isn't as good as this move. Default Gunner relies on this move a lot, and it even stands up to the other viable neutral B in a customs setting.
Throwing out any hitbox won't cut it. Wario's enlarged head is completely invulnerable. Throw an attack at it, and you'll get chomped, even from several steps away. You need a move that's disjointed and properly spaced to beat him, or a sword swing. And the constant hitbox makes this a great move to cover ledge options, beating everything except ledge roll, which has enough endlag that wario can close his mouth and attempt to grab them. And that intangible head makes letting go of the ledge and jumping up with an attack often fail depending on what your character has to use from that position. It's a great move even before you look at eating opposing projectiles and your bike. The normal startup is frame 8, but he can eat items on 2, that's faster than most reflectors.