As I mentioned above... the technical manuals are NOT considered canon therefore, they cannot be taken at face value.
Also, despite that a photon torpedo is claimed to contain 1.5kg of matter and 1.5kg of anti-matter... it doesn't automatically mean the explosive yield will be 64 Megatons (and no, I am NOT implying it would be lower than that either).
On-screen data is inconsistent at best (as we have examples of both low and high very high yields), but throughout TNG, DS9 and VOY, we've observed effects of both phasers and photon torpeodes as being excessively powerful (in the hundreds of megatons, gigatons and even teratons).
Furthermore, what we need to keep in mind is that all Starfleet hardware (weapons included) use a plethora of subspace based technology.
Why is this important?
We've seen that subspace technology was applied in every field in Trek. All ships emit subspace signatures for example and use low level subspace field to lower their mass to the point so they can maneuver like small fighters and greatly increase sublight speeds - a prime example of this is DS9 pilot episode in which O'Brien was tasked to create a low level subspace field around the station so the stations orbital/positioning thrusters would get them to the mouth of the wormhole by next day - and even O'Brien mentioned that the station is not a starship, meaning that ships do this all the time - and we've seen them do this).
So, it stands to reason that application of subspace technology can explain 'Gigaton' and 'Teraton' level yields from Federation, Klingon, Cardassians and Romulans even.
In short, applying subspace technology to weapons (phasers and photon torpedoes) could conceivably have an effect on energy output and explosive yields, amplifying both to very high levels.
This is something most people seem to ignore even though we witnessed both Phasers and Photon Torpedoes utilizing subspace technology (and considering the feats we saw from both - as well as how they interact with various substances, there's easily enough leeway to explain why the effect would be minimized or enhanced even - the TNG Pegasus episode is quoted as an example of low yields, but we knew nothing about composition of the asteroid in question which could reduce effectiveness of weapons - various substances in Trek can be used to minimize destructive effect of phasers and photon torpeodes).
Also, it doesn't make any sense that 64 Megatons would be the top end yield for 24th century photon torpedo.
It would barely make it more powerful than current day nuclear weapon - which simply doesn't keep track with 360-odd years of exponential developments.
We also know that Starfleet weapons are highly customizable and seem to exhibit a shaped charge effect (focusing the energy output or even explosions to a singular point as much as possible - which easily explains why weapons would behave like 'firecrackers' as opposed to produce ridiculous shockwaves all the time).
Furthermore, SF could have designed their weapons with specificity to the point where they wouldn't produce much fallout.
And, we know both Phasers and torpedoes can be used as precision tools.
In fact, most of the times when these weapons were used, they had to be calibrated very carefully to avoid potential fallout effects on a planetary surface and wipe out sentient life on it.
In the case of the Enterprise-D, it bore thousands of km deep hole in seconds using a very low (and tightly focused) phaser beam, which would have required gigaton yields in the first place - and other cases used even lower yields (which required weapons to be set to such levels in the first place to avoid catastrophic fallouts when used on planets, etc.).
So, while the weapons on-board Federation ships may not require large quantities of energy to run, through use of subspace technology they could exhibit orders of magnitude higher effects - depending on how they are calibrated.
As for yields being measured in 'isotonnes' in Trek, well, that could easily (again) be attributed to use of subspace technology.
Plus, why assume that Starfleet would be using same measurements as we do right now?
Its set centuries in the future, and it stands to reason that various measurements could undergo changes as well (however minor they may be).
I understand we are trying to put things into context based from our perspective, but I'm just saying that for whatever reason, Starfleet might have decided to use different measuring systems as a direct result of using Subspace technology and have changed terminologies as a result.