You can't even fault them for it, or any musician. The problem is, when you sit at home and futz around with your instrument sound, you make sure it sound round, and has a lot of body. But, what you are designing is a solo sound, i.e. as if you were playing all alone on the record.
Once the other instruments come in, your guitar sound's bottom end totally gets in the way of the bass. So, the solution is to EQ the hell out of the guitar to confine it to the frequency space it belongs in the mix.
That said, that is of course a beginner's problem, and doesn't apply to DT, who have been recording for 30 years.
My pet theory what the real problem is that there is no overall orchestration going on anymore, i.e. there is nobody saying "too many instruments are playing; MM, play something less busy, JP, maybe you shouldn't do anything at all in this section". Kevin Moore of all people once made a comment regarding that towards modern DT, that he thought everybody in the band was just playing their own thing, with little communication.
So, with everybody playing at all times, you can't ever give any of the instruments body because they will clash, and thus are forced to limit all of them to very narrow confines in the spectrum. I think that is one of the reasons why DT's late albums have been pretty compressed (which is another way of dealing with the problem), and the drum and bass sounds are very thin. It's all coping mechanisms to deal with a crowded frequency space.