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I believe that it is likely to have better absorption. OTC estrogen has often been indicated for vaginal use and I think that they probably put this aspect as primary in terms of not changing the environment or flora. Estrogel is indicated for use other than the vagina and breasts so it is based more so on skin absorption via the underarms or wrists. I do believe that topical estrogen can have substantial effects on hair and skin beyond those of just the increase in serum estratradiol but we have few tests, if any.How much more efficacious do you think estrogel is compared to biestro @JaneyElizabeth ? IIRC estrogel has twice the estradiol but what other differences are there?
Both, if used on genital skin are likely to go much, much farther in terms of having to use much less of the medication which can result in substantial savings. But given the possibility of topical improvement, I recommend use on the scalp for men and on the breasts, buttocks, thighs, neck, face and scalp for MtF's along with on genital skin/scrotal tissue. Probably a balance of both is best.
However, I know where the meat of the question goes. So, say minoxidil appears to work topically in its non-oral form without increasing hair in other places for most people. Some do experience hypertrichosis but largely minoxidil is seen as having localized effects and some meds work like this. Estrogen appears to have both localized and systemic effects and so the goal is to, for guys, to get the localized effects without the systemic ones. I go back and forth as to whether this is possible and it is the crux of the matter. So assuming most meds go at least a little bit systemic, what's the likelihood of estrogen's benefits on the scalp being curtailed to that area. It might be possible but it appears to be a delicate tightrope between getting no results and getting full-blown feminization. The truth is that we just like knowledge about the many permutations of how HRT works in terms of cycling/taking breaks and how long things can be maintained without the med. Dutasteride is especially important in this scenario.
So, I hope that many folks will find that the localized benefits are worth it and curtailed to that area but my guy feeling is that oral minoxidil is the better choice for those who want to remain "all male".