There is no safe position in landing craft
Impression that people often get from the movies is a group of soldiers standing (sitting) safely behind closed doors(ramp) in a landing craft. But once this ramp lowers, first to get out are first to be killed. As with most things in Hollywood, this impression is quite wrong.
If we exclude naval mines (which were sometimes present), first thing that would "greet" landing craft from the shore would be artillery fire. Depending on circumstances, this be could coastal batteries, mortars, AA guns of various caliber etc. As a rule, there was no armored protection against that . Even larger ships (up to the destroyer) were not armored against such threat, because if they were they would be significantly heavier, with larger displacement and slower, possibly not seaworthy. Therefore, landing craft relied on their speed and prior suppression of defenses to avoid being hit. Naturally, as they came closer to the shore, enemy fire was more precise, and as they stopped to disembark troops they were one fat and juicy target. Therefore, lingering in standing landing craft was not most healthy thing to do. In any case, when directly by let's say mortar round, it would be hard to tell which position in landing craft is more safe then others.
What about machine gun fire ? Two most used landing crafts used in WW2 to deliver roughly platoon of soldiers were American LSVP and British LCA. LSVP was practically unarmored, made of plywood except the ramp, therefore susceptible to rifle caliber fire. Idea was to get in and out quickly as LSVP itself was not safe from machine guns. Even with the ramp in upward position, bullets would come from the sides (machine gun nests usually set to deliver flanking fire and crossfire). LCA on the other hand has some armored protection, especially sides and front ramp. Overall, it is considered to be better landing craft then LCVP although worse vessel as it slower and less seaworthy. At least theoretically, LCA would protect occupants from rifle caliber bullets and shell splinters coming from sides and front while the ramp is in upward position. Sitting position would not matter much, as there were no special more protected spaces inside LCA, except perhaps for members of the crew who would not land anyway. Overall, theoretically you would be tempted to stay inside if there is small-arms fire coming, with caveat that LCA would not be much of protection against anything larger then 20 mm . Indeed, many of LCA's were sunk during WW2.
What happens when troops disembark ? Usually, landing craft would attempt to deliver troops as close as possible to shore. However, depending on terrain, soldiers would often have to walk considerable distance trough waist deep water (or deeper) carrying all of their equipment and under fire. In such circumstances it is hard to tell who has better chances: one that goes first and tries to get as quickly as possible to the shore and some cover, or the other who waits in landing craft few dozens of a second before disembarking. Luck would also play its part: enemy gunner could be targeting landing craft immediately as it comes to the shore, or noticing it only after ramp lowers and first soldiers move out.
Therefore, as a final conclusion, we could say that safety didn't influence position of soldiers within landing craft. More likely it was dictated by tactical needs for particular landing, for example few rifleman first, then those assembling Bangalore torpedo, then machine gunner etc ... Overall goal was to move everybody as quickly as possible to the shore, and have them take positions for their assigned tasks.