In the late 19th century there were a lot of blanks to fill in and not enough experts to cover all the bases they had. Automobiles and airplanes weren't even a thing yet. Because of this rare supply-demand relationship many experts could afford to make a lot of gambles and guess alongside of their solid works of scientific research, many of them mixing guesswork with hard earned knowledge. Nobody was going to fact check them either. They knew this. I'm willing to bet that Darwin knew it. If a professor in this modern world took as many liberties and chances with their research as the classical ones did they would be harshly criticized.
How could someone truly know if life first formed deep below the surface on thermal vents or near the surface in stagnant pools of mineral rich water? That would be a tough one to prove one way or the other. Perhaps they formed in both manners simultaneously.