I agree with you "skips the first line, kinda the hard way.".

I would advise the OP to use:

my $discard_first_line = <FILE1>;
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before starting the while loop.
The more cryptic albeit simple: <FILE1>; would work also. I prefer the extraneous "my" variable because it is very "cheap" and it is clear what it does. I would personally write a comment like <FILE1>; #discard first line anyway.

I agree with your other points, except that as written $info2 = $hash2 -> {$prog} -> {info2}; doesnt hurt either, it does that when the -> is assumed in $info2 = $hash2 -> {$prog}{info2}; anyway

My point is that there is no need at all for a 2nd dimension on the first hash, and no need for the 2nd hash at all!