I agree that the implementation is very loose, which is a likely result of representing a complex idea in a crossword. One could get round the problem raised by Meursault by jumbling each answer first in a particular sequence so the thematic letters are adjacent and in order, then replacing theme with the other half of the equation, but that is not what the preamble says.
As for the other thematic entries, while I could see that a reduction of L's could represent the contraction of length predicted by the theory, I couldn't really see how added T's could signify the slowing down of time at high acceleration. I'm no scientist, so perhaps I've got that wrong.
I'm happy to grant the setter some licence and credit for an ambitious and unusual theme, but my feeling reading comments here and elsewhere is that he has a left quite a few solvers a bit perplexed.