Hmm, I think that you hit the nail on the head when it comes to my problem with some of the rules in the later editions of Traveller.
These are some of the earlier threads I posted covering design sequences from or derived from MegaTraveller.
http://www.travellerrpg.com/CotI/Discuss/showthread.php?t=29055
http://www.travellerrpg.com/CotI/Discuss/showthread.php?t=27245
I read through these. There are some issues that could be called (and I will) "glaring inaccuracies," such as the number of crew needed per area of sail. Others, such as the shaped charges before TL7, perhaps "improper terminology," in that I think they meant shaped charge munitions as we think of them today.
Finally, I'm fond of invoking the "unspoken caveat" concept, and I think it applies to the 1 crew per kilogram of ordinance rules. Regardless of them applying it to all pre TL4 vessels, they meant it for ships of sail of the wooden hull and before era, and lumping wrought-iron armored vessels, with guns to match, breaks their algorithm. I'm have no idea if lumping those in with TL 4 makes the numbers work out better, but I'm guessing that that's the psychology behind it. Given that they are lumping everything below a certain level together, they are putting ballistas in with early cannons, so the exactitude of that rule is clearly pretty vague.
Based on what I have in my library and photocopy collection*, the level for breaking "my willing suspension of disbelief" is pretty low.
*first of all, did you mean a library and photocopy collection of game rules, or of historical naval weights and measures?
Either way, I believe that therein lies the true crux of the situation. You have a library of accurate weights and measures of boiler masses of late age-of-sail/age-of-steam naval vessels and are comparing it to an all-tech-level vehicle builder for a science fiction game(s) most concerned with giant contragravity spaceships. That makes you close to singular. Neither the people who designed the system, nor the people for whom they were expecting to use it, have that specific expertise or focus.
The counter-argument of course is: if they didn't want people going over their measures with a fine toothed comb, why did they build exacting wet-ship design rules? All I can say to that is, well, it's a discontinued line and you'll notice (if what I hear around here is correct), that the T5 builder affords itself a lot more vagueries.
I'm certainly sympathetic (perhaps more than a previous thread would indicate). Over on Dragonsfoot, we've had a rollicking discussion about the nature of longswords, shortswords, and bastard swords. I have to remind myself that the game isn't a historical emulator, it's a sword-swinging, treasure-getting game.
I think your best bet is to, as it was hinted at in those previous threads, make revisions as you see fit, and, if you so desire, submit them as potential errata. I don't have solid numbers on how many people still play MT (and check here for updated material), but there might be others who would appreciate it.
One of the reasons that I like Classic Traveller is that it does not attempt to go into a design sequence for anything except space ships, and then only the larger ones. I still need to work on a better design sequence for small craft that makes them more affordable, while at the same time being simple and easy to use.
That is certainly a design decision that makes it significantly harder to quible with. Modelling systems tend to break down when they hit scales for which they were not intended. Saying, "over here there be dragons" innoculates people from from criticism for not designing a working model for areas they aren't concerned with.
If you come up with a smallcraft system that works, I'd love to see it.