The problem with the Field Manual RATs is that they suffer from a bad case of codex creep; the Free Worlds League and Draconis Combine are heavily outclassed by the remaining Houses, so using those RATs to determine forces puts them at a serious disadvantage. Several units are also at too low (much more rarely, too high) a supply rating to obtain machines they are supposed to deploy in numbers- the Legions of Vega, for example, cannot generate the No-Dachi they are supposed to have in the greatest concentration at the time.
The RATs in FM: U are even worse, with the Federated Suns' chart being massively superior to everyone else's, to the point that an AFFS militia-grade unit is statistically likely to generate units of a mass and technology rating equivalent to or better than what is offered by the best-supplied elite formations of other Houses. The discrepencies between better-supplied AFFS units and those of other nations is even more glaring. Until ColBosch issued an errata ruling to remove the text from Total Warfare referring to it, the Field Manuals were advised in favour of the RAT presented therein. TW's RAT should statistically generate forces that are reasonably close in technology levels and mass*.
Then there's the tables in the new FM: 3085, which has things like the Morgenstern fighter on the WIE charts but not on those of the LAAF which commissioned the design.
Obviously there are only so many slots to go around, but...
I would be happier with RATs if units from the same supply rating generated similar results for technology level and mass, ie an A-Rated DCMS unit should have a reasonably similar level of technology deployment to a comparable one from the Capellan Confederation, Free Worlds League, or whatever. If you want to have underdog fights it is still then possible to use lower supply ratings, different experience levels, and so on. Admittedly Periphery and Mercenary lists will and should suffer in comparison.
That said, I can imagine the horrors of trying to set up tables that provide such a result.
Some RATs can be used as a good way to get a feel of what a faction or unit may be deploying on top of material in TRs or individual unit entries. Some RATs are also less than helpful in that regard, especially if you find yourself on the receiving end of the imbalance between factional RATs.
The MUL is a solid source, but it is ultimately a binary yes/no availablity list. On the one hand, that's exactly what it is for; on the other hand, a Common/Uncommon/Rare frequency entry beside the availabilities would be a good feature, one day.
*RAT analysis spreadsheet for FM: U and TW below.