FOlks, as I said Marvel did a rethink. Prior to Secret Wars III (i.e. the plot run in FF), it was thought that LT was just another cosmic type. After that, Marvel had made him top dog. Marvel Continuity is NOT continuous.
Beyonder WAS the top dog during the day. LT and all the other cosmic types were too SCARED (this is explicitly stated in Secret Wars II #8 and #9, I think), to do squat against him. Only Owen (Molecule Man) had the guts to stand up to him.
Later, when doom, Kubic, Shaper and owen show up in Beyonder's pocket universe (the one where Molecule Man put him in when Beyonder made himself mortal in SW II #9), we find out he's not all that.
I don't know when LT was made top dog, but it certainly was that way as of Thanos Quest, and most recently it has been explicitly stated by Thanos himself in Marvel Universe: The End.
So, original beyonder vs. current LT, I dunno...it's too confusing to tell.