Absolutely. The first to file system greatly disadvantages individual and/or poorly funded inventors, because for big corporations, the cost to file is no great hurdle.
Flip side: first to file arose because first to invent is inherently ambiguous. The fixed cost of a filing was deemed better than the large and unknowable cost of determining who invented what when through the courts.
Proof of independent creation might be; but similarity provides a statistical test of that. Cases use similarity and probability, they don't take "independent creators" at their word.