There is almost a confirmation that Maya was pregnant during Baby Finches flasback. We've been told in 0.35 that Maya didn't have an abortion she told she had
This is a weak point of this theory. Technicaly, it might be imposter Ami, but imposter Ami theory is a big assumption itself
Connections with Ayane and Himawary aren't clean enough too, because after rework Himawary is introduced before Ayane's pregrancy. AFAIR, the only reasoning underneath "Himawary is Ayane's daughter" is existence of some special connection between them.
About Makoto's offspring - we have BigBoy
And why Makoto's apperence on rooftop was getting zero buildup? Selebus
In this case Ayane would not get to the roof during fith reset