What is it that actually bothers you with the first sub? The   return \@gencli; is about the cheapest way there is of returning an array from a sub - which one way or another is what you are doing.

I would be much more worried about the potential confusion in the mind of a reader of the code caused by overloading gencli three ways - as a sub name, a scalar containing a file name, and as an array.

Note too that using & to call a sub is generally frowned on except in a few rare special situations where the calling sub's argument list (@_) is to be passed into the called sub or you wish to ignore a sub's prototype.

The two lines:

my $gencli_scalar = gencli();
my @gencli = @{ $gencli_scalar };
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might be better rewritten:

my @gencli = @{gencli()};
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(although I'd use a different identifier for the array). However, generally there is probably no need to actually copy the array at all, but simply dereference the array reference returned by the sub as required.