Does the light beam layer over the eggs in Alien make sense after this film?

Could well be that we're meant to assume it is some sort of safety device, much like the one that is removed from bombs so that they are armed. Prometheus seems to suggest in its own vague way that there are similar safeguards in the 'temple' / urn chamber. nothing rots in there, not even a 2000 year old head, that isn't eaten by worms - who seem to have been dormant until disturbed by humans. Kane walked THROUGH the light beam, and so part of his body was below it, and close enough for the Facehugger to detect him.

The Derelict is much older than the Juggernaut, and the Juggernaut has a cargo hold full of urns and hyper sleep chambers on the bridge, then in Prometheus we see a more updated ship, and in my opinion the Urns are more stable than the eggs and are technically more easier to carry.