Sentence Correction

Geologists once thought that the molten rock known as lava was an underground remnant of Earth's earliest days, sporadically erupting through volcanoes, but they now know that it is continuously created by the heat of the radioactivity deep inside the planet.
(A) was an underground remnant of Earth's earliest days, sporadically erupting
(B) had been an underground remnant of Earth's earliest days and sporadically erupted
(C) was an underground remnant of Earth's earliest days, which sporadically erupted
(D) would be an underground remnant of Earth's earliest days that sporadically erupted
(E) was an underground remnant of Earth's earliest days, having sporadically erupted

OA is A

My question is [spoiler] the explanation says 'was' is correct and 'had been' is wrong because there is no two actions here. But, can 'Geologists once thought' be considered action-1 and 'molten rock an underground remnant' be considered action-2, and that action-2 happened before action-1. And hence we can also use 'had been'?
I understand the later part of the answer i.e., 'sporadically erupting' is correct and from that we can eliminate B, C D & E and hence arrive at A. But what if we had a choice exactly as A, but had 'had been' instead of 'was' ie.,
(A) was an underground remnant of Earth's earliest days, sporadically erupting
(B) had been an underground remnant of Earth's earliest days, sporadically erupting
Which one would you choose and why?
[/spoiler]

Question source: Manhattan