My own version. Any speculations are welcome.
Remilia and Flandre were born in the 1500's in France from the Scarlet family which is from the Dracula bloodline. They lived in a mansion and served for their lives. Remilia is treated like an heiress, being the eldest. While Flandre is always playing with the servants. Because of this Remilia lives under heavy restrictions. She didn't like it, really. But then after discovering each abilities, Remilia controling fate and Flandre destroying everything, respect for Remilia increased and Flandre was immediately causing panics and the family ordered the servants to lock her in the underground basement. Remilia, of course, was against this because she cared for her sister but was forced to obey and was convinced to actually agree.
After years (now it's the 1700's), the French Revolution began. The Scarlet family was involved and eventually died, in exception to Remilia and Flandre. The two of them escaped after the soldiers of the war came in and killed everyone there. They found a mysterious portal (gap, perhaps) and entered it. They then gain powers and respect from certain people and build the Scarlet Devil Mansion.
How does Sakuya's backstory relate? Jack and Sakuya moved somewhere else, which is Gensokyo. They figured there'll be more things to kill than just vampires and humans.
Oh god, so much Merc headcanons.
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