The second youngest iteration of the Temple of the First Dragon was built for a congregational period of the dragon cult’s history, as they were enjoying a revival of sorts. The largely neglected pews (B) may indicate that that period is gone and that this level is now largely unused except as a offices (E) for those clergy who minister to the pilgrims on the level above or defend against looters.
In order to support the new structure above, the main altar and statue (A) were removed to the new top temple and replaced with a large pillar and stairs. Additional supporting pillars were added among the pews (B) and in hallways (C, E). The doors that accessed this level when it was the top one were barred and buried. Small creatures (perhaps giant rats or giant ants or whatever) have made their burrows beyond these doors (F) and may become aggressive toward anyone lingering too long in the chapel.
What was previously a secret entrance for clergy (D) is now an isolated hidden chamber where lesser sacred relics are kept. After all, few yet descend to give their offerings themselves, let alone receive the blessings of the First Dragon in person.