Agreed that the "BoT" weapon was an obviously customized anti-installation weapon. Perhaps we should think in terms of warheads here: in the real world, naval guns have armor-piercing ammunition for use against other warships, and shrapnel ammunition for use against shore targets. The "BoT" weapon might simply have been a standard torpedo weapon of some sort firing an anti-installation warhead (the equivalent of a battleship gun firing gigantic shrapnel ammo), or more probably a modified weapon optimized for this kind of ammo (the equivalent of an immense howlizer on a monitor-type vessel, basically useless for antiship use no matter what ammo, but optimal for firing shrapnel rounds ashore).
However, I'm not generally fond of the idea of the "BoT" weapon being a classic guided torpedo as such. After all, it's never referred to as such in the episode. IMHO, "plasma torpedo" is a classic Trek torpedo with a plasma warhead (whatever that is), just as shown in DS9 for the Cardassian planetary defense platforms. The weapon in "BoT" in turn is an entirely different type of weapon - although having the same basic sort of warhead, it scales it up to ridiculous proportions and uses a different delivery method for it.
The guidance and acceleration properties are quite possibly separate from the warhead. I see an analogy to the SARH air-to-air missiles of today, such as the widely used AIM-7 Sparrow: the mothership has to keep a beam of sorts locked to the target to deliver the warhead which is incapable of independently tracking the enemy.
The firing procedure could be like this: generate the deadly plasma by activating/detonating a standard "plasma warhead"; spit it out; accelerate it using a forward-projected warp field; if the enemy tries to dodge, turn the accelerating warp field like a flashlight beam, and the warhead slavishly follows within the beam.
Such technology would seem quite practical and fitting for the Trek milieu: the navigational deflectors already behave much like this putative accelerating field.
Timo Saloniemi