The only reason Beyonder was made that powerful was by his creator Marvel never intended him to be that they said the writer over step his bounds by making him that powerful.
"The Beyonder was a controversial character amongst creators. Creators felt that Jim Shooter had abused his role as editor-in-chief, and forced the use of the omnipotent character upon other writers and editors. Some critics felt the crossovers didn't always mesh well with the main book. One of the most vocal critics was John Byrne.
Apparently, Steve Englehart wanted to tie in the Beyonder to older characters known as the Beyonders (first mentioned in the team-up comic Marvel Two-in-One #63, beings powerful enough to collect planets) for his "Secret Wars III' story in Fantastic Four #318-319. According to Englehart, editor Ralph Macchio hated the character and ordered the Beyonder "removed" from the Marvel Universe. Englehart did as asked but has stated that he tried to exile the character with dignity. The character was subjected to a retcon making him less potent that originally determined, and explanations of his omnipotence have been written off as the more powerful beings "playing along" because the Beyonder's role was pre-determined".
Retrieved from "http://en.wikipedia.org/wiki/Beyonder"
http://www.killermovies.com/forums/f95/t412978.html
Beyonder at one point, when regaining his powers was stated to be "millions of times more than all the powers of the rest of the multiverse combined"
Pre-retcon was more powerful that LT whos powers were limited to the Multiverse.
I honestly don't remember if beyonder actually fought LT. But however if you look in the above scan posted by Mordum, every being in the universe, pretty much including LT, gave reverence to Molecule man, and safe passage. They respected him, and asked that he do what they couldn't. To defeat the beyonder. In the site I provided, the two fought, and the reprecussions were seen across the multiverse.
Please look at the beyonder respect thread I provided above. It was excellently done by those who helped to provide it.