Neither Horimiya nor Lv 999 Yamada-kun is unambiguous* that I can recall, but imo they don't leave much doubt that it has taken place between the MCs.
* - Even that which I'd call unambiguous doesn't literally show the penetration itself, but a rare few that I've seen (like DomeKano or Kimi no Iru Machi, with Aku no Hana being the most extreme I can recall) don't leave any reasonable doubt that it's taking place.
Well, it's been a while since I read it. I also have a shitty memory. Probably worth rereading it.
Wait, Kimi no Iru Machi? It may have been six years, but is my memory
that bad? I'm certainly
not that dense... Another one I will have to reread.
However this manga has a somewhat different "feel" to it. It "feels" more like one of the ones that basically ends when the MC gets together with whomever he chooses (i.e. those "harem" that isn't actually a "harem" ones) but because they clearly have gotten together and it hasn't ended, it probably will before/when their relationship reaches a certain point. Basically the point of the manga is to keep people holding on for the "climax" of the relationship (w/e that may be in this case). I could easily be wrong, but there is already plenty of evidence for this.