Penis ≠ Male
Lack of penis ≠ Female
There is more to this world than black and white, male and female, etc.
Although given that it says in the story that the penis just suddenly appeared, you can't honestly count this sort of thing as representative of real-life women with penises (men without penises, even less so).
This is true. Although I find futa penises to be so bizarre, both in circumstance and anatomy, that they may as well be toys with extra function. In which case there really is little impact on the gender of the character they're attached to.
To be honest, it's the futa stories where the girl comes off as more "trans-like", such as that HonoMaki one, or where it's a magic/science dildo with extra function as you say, such as in Happy Cherry 2, where I can accept the idea most easily. The ones where it's just the artist is clearly going "I want a dick in there, but I don't want a dude" are more difficult for me to accept.
But then, previous discussions here have shown that a lot of folks don't even like toys in their yuri porn. I'm a lot more accepting than the norm for those, I think.