My understanding of what Shyheels said is that men should be able to wear, visibly in public, long boots (I assume not above knee-high), even if with flat heels. That implies that they can/should be worn over full-length trousers or leggings etc. I would tend to agree; long 'fashion' boots on men should be just as acceptable as those for protective reasons, whether worn outside or inside trousers. Boots reaching above the knee are for separate consideration - but they could also be considered as suitable for male wear, at least in a fashion context, but perhaps with less of a justifiable recent history (quite apart from unavoidable fetish overtones). Any such boots with heels is another matter; heels on any type of 'male' footwear are not generally accepted (as we well know) and boots, of any length or style, are not outside this prohibition, with the obvious exception of cowboy boots, cuban heeled 'Beatle' boots etc.
I agree that wearing long boots inside trousers etc may effectively hide them and thus remove the objection. But there is no more point to doing so than there is to wearing high heels almost hidden under extra-long trousers - except to please the wearer whilst not frightening the neighbours. And, if a good reason for long boots is protection against the elements, snakes and other hazards, then putting vulnerable trousers over them is not a very good idea. Isn't a need for a modicum of such protection a valid reason for long boots on men or women - which is why we wear non-fashion wellies in the rain or mud, or functional riding boots? Long boots don't have to be extreme high-fashion to look good and also give that extra protection and warmth that may be needed.