Indeed - the illicit Starfleet interphase cloak from "The Pegasus" made objects intangible as well as invisible, but that was explictly presented as Different.
[Compare Rom & Quark being able to carry a cloaked Klingon cloaking device in DS9: "The Emperor's New Cloak" - while complaining about the weight, no less!]
That cloak might have pushed the ship into subspace. If it phased through the asteroid, the rock should have passed through the ship, leaving the crew unable to breath. However, if it went into subspace, it could go through the asteroid without the asteroid going through it.
It was explained very simply in 'Balance of Terror' that the Romulans' mega-weapon used so much energy that they would have to become visible to use it, not having enough power to do both.
In contrast, we never heard anybody speculate that the Romulans decloaked whilst firing because they didn't have power to keep both the cloak and the plasma mortar going. That's pure fan speculation - and quite possibly untrue. Kirk merely says this decloaking maneuver is "perhaps necessary when they use their weapon", and seems to be right about that, but the reason for the necessity is never revealed.
I'll admit I don't consider NEM all that reliable in some tech areas.But in TUC it was clearly stated the Klingon conspirators had gotten around that basic issue
I tend to view it more as an issue with the energy the firing system uses than the torpedoes themselves, since there's no evidence that the Kingon movie torpedoes are plasma-based like the BOT weapon
As for TMP, that's one aspect I tend to disregard as well. The novelization does flesh it out a little better than the film but I still think it's a silly circumstance, and it's a repeat of the torpedo problem in "The Changeling."
), and then says the ship can withstand three more such attacks before the shields fail completely. That'd require a minimum of 360 photons to disable the shields on a Constitution class ship, let alone damage the hull itself. At the time the episode was made, a lot of details about technical aspects hadn't been nailed down yet, including the composition and relative strength of the photon torpedoes. Looking at it from a more modern perspective and going by what's been established in later series, Spock's statement seems pretty silly.
But of course the movie would been over rather quickly if they'd been disintegrated. 
But in any case, you speak of the Enterprise's survival against V'Ger in terms of 'power', e.g., the Enterprise should've have survived because V'Ger was more powerful. Power requirements aren't everything. A point-defense system on a modern military ship protects itself from enemy missiles by tracking and shooting them down mid-flight with relatively basic gunfire, something that requires less 'power' than the offending missile. Offense in defense isn't a pure pitting of energy levels. We don't know what sort of offense V'Ger launched and how the Enterprise screens worked. If I may milk my fanon notion that the Enterprise screens were a response to the Romulan weapon from BOT a little more, I'd suggest that V'Ger was attempting to 'scan' the Enterprise in the way it did Ilia - a sort of scanning that necessitated breaking down the ship and its constituents to the basis of particle and energy levels. This destroyed the original, of course... in practice, this may not be a terribly different process to what the Romulan weapon wreaked on its targets - total disintegration, according to Spock. Hence, when Starfleet invented a shielding technology against Romulan disintegration, it fortunately stumbled upon a defense against V'Ger's scanner as well. There's still the issue of raw power at play - the Enterprise couldn't resist another attack - but things aren't necessarily as simple as 'who has more power', and the fact that the Klingons succumbed more easily to the weapon can say as much about defense tech as power levels.I'd disagree about the modern BOP lacking a torpedo tube in TSFS or TFF; I think perhaps the modeling details might have been slightly different (I can't recall exactly at the moment), but the effect in TFF seems pretty clearly intended to be a torpedo. The TSFS effect seems a little more like the disruptor bolt effect (used on ships like the Vor'Cha) according to the TrekCore screencaps, but it's harder to judge without the motion naturally.
My theory, written out in more detail above, was that the Bird of Prey in TUC didn't have to uncloak because it was using Federation torpedoes (to frame the Enterprise) instead of the energy weapon used in TSFS and TFF, hence no power requirement concerns.
I like to think the non-physical torpedo used in those two movies were the same weapon used in Balance of Terror. Federation shields/screens have advanced since BoT, hence the reduced effectiveness (see TMP's line about 'new screens').

I've been toying with an idea regarding the multiple warp cores talked about on the STXI threads. What if Chang's BOP had a second dedicated warp core just for weapons?
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