I wonder if you are failing to see the forest for the trees.
The question is, Is penis size hereditary?
Well, what is heredity? The transfer of characteristics from parents to offspring. Now, traditionally, we have assumed that what is hereditary is entirely a matter of genes. More recent work, which you explain in general terms, suggests that far more than genes are involved. You mention non-transcriptional RNA, alternative splicing, RNA editing, and so forth.
Assumptions of a few decades ago are now seen as decidedly passé. We know more now, but our current assumptions, just like our past assumptions, will no doubt be subject to correction and themselves come to seem variously incomplete, misconceived, or outright wrong.
But what difference does this make?
The question is basically asking, Does Jones likelihood of having a large penis increase if his male forebears had large penises themselves?
The question could equally be about small penises, or large/small noses, or any of a huge range of physical traits.
And without having any clue of what a gene is (and remember, Mendel himself had no knowledge of what genes are), we could say that yes, the likelihood of having Trait X, lets say, increases if that trait was present in ones forebears. This is a principle that has worked in animal husbandry and crop development for centuries, and which humans have long observed, informally, in traits visible in their own offspring. You surely have seen this yourself. Tall parents are going to have, as a rule, more tall children than short parents are.
Now, if you say, correctly, Ah, but the mechanism of how heredity achieves this magic is incompletely known, is still under study, one could sagely nod and agree, yet still insist that heredity, broadly defined, is not at all disallowed as a factor in cross-generational transmission of traits.
This mechanism will always be under study. But wherever it takes us, it will still be endeavoring to explain why so many traits are inheritable.
The question of exact mechanism is scientific, and unrelentingly in progress.
But the basic question is long-answered and philosophical. More scientific detail may shade it but not significantly alter it.
At least, that's how it seems to me.
How 'bout it?