The two versions have different stage orders and probably other changes.
Someone was kind enough to inform me that Lethal Thunder is essentially the novice difficulty version of Thunder Blaster, so I tested it myself - now I understand why some people sneer at the difficulty of the game with autofire, Lethal Thunder is indeed a mere shadow of Thunder Blaster:
- Instead of checkpoints, there are instant restarts. Considering that there are no power-ups, only different weapon types, this alone makes a huge difference.
- Every remotely dangerous constellation of enemies is either absent or altered in Lethal Thunder. The deadly asteroid shower in stage 5 (stage 1 in Lethal Thunder) is gone, bulky enemies that come from behind in Thunder Blaster come from the front, so do bosses etc.
- Enemies fire a lot less, and slower. They are also not as resilient.
- Bosses have almost no health, one or two tossed pods are enough to wipe them out.
- They also have severely reduced patterns on top of that, some of their body parts are either entirely or almost useless.
Just to compare: Lethal Thunder with autofire is even easier than one loop of Fire Barrel (which is otherwise the easiest Irem clear) whereas Thunder Blaster with autofire is the hardest 1-ALL by quite a stretch. It's that huge a difference.