Chapter 8, with Honey automatically assuming that a boy has possessed her mom's body (instead of, after seeing years worth of odd behavior and other hints, thinking that there could be another reason), paints a pretty clear picture that Honey has never suspected anything at all about her mother's identity.
Flash Back - Teri and Brady in the Cat & Butterfly arc. Recently, Bay's early days at the SailorSun.com studio.
However, a few comics and her feelings in general hint that she really is a girl inside (or became one over time) and is very comfortable in being so. Is this a case of The Mind Is a Plaything of the Body, or something much more than that? Bay also shows a strong maternal instinct towards Honey.
Going Native - It's becoming increasingly more obvious as the comic progresses that this is happening to Bay, to the point where she's starting to not mind and is accepting it. Also see Love Epiphany below.
Informed Ability - Honey is supposed to be a genius, but she doesn't even pick up on Ams speaking Pig Latin (though she was waking up after undergoing what was essentially massive genetic manipulation at the time). Essentially, other than really barely-above-average booksmarts, she never shows the kind of quick or deep thinking her given IQ should entail.
Karma Houdini: any number of cheerfully irresponsible idiots, but Chris from the studio really takes the cake.
Kid from the Future - Honey. Recent events have revealed that Brady, who looks like a younger version of Honey and also calls Bay "Mom" was snatched from an alternate future as well.
Love Epiphany - By the looks of it, Bay has finally admitted it to herself, going as far to kiss him◊ later on. She also admits to Shaura that she liked it and that it is 'like a crush that won't go away'.
The Auction Guy seems to also love Bay back, but Bay is torn over who she was, is, and will be and doesn't know what to do.
Mundane Fantastic - Among other things, switching genders and Time Travel don't seem to be rare occurrences and are quite easily accomplished (making Honey's obliviousness about her mother even more counterlogical). There's also the HRC, which is in effect a computer system that can edit anyone in the world, also with little effort. Our Earth this definitely ain't.
No Name Given - Auction Guy. Even on the cast page he's just "Auction Guy".
Omniscient Morality License - While nowhere near omniscient, the producers seem to have this act down pat: Need an actress? Turn your actor into one using illegal future-tech that may or may not be a felony! Need action? Grab some green slime that is used in more 'illicit' films with various undefined properties and some-such. Need a sidekick for your TG'd main? Just steal her unborn daughter from the future, not like they'll care. More amazing is that before they randomly decided to go bankrupt, no one questioned this ever: at the very least their accountant should have taken notice. Why? So we can produce a televised adaptation of a Sailor Moon fanfic. Internet IS serious business.
Off Model - Some comics clearly have much more work put into them than the rest, while others seem to be obviously rushed.
Pet the Dog - Despite being The Rival to Bay who's not above cheating to win at stuff, Morgan still is quite kind to Teri when she finds him lost and scared in the streets. She brings him home, cleans him up, and feeds him caviar, as well as planning to get him pancakes if he behaves while she goes out.
Plot-Induced Stupidity - Honey, despite supposedly having an IQ of 352, rarely shows it and often has to be bailed out and/or scolded by her mother for the trouble she gets into. She also never seems to notice or get any of the hints about Bay's former identity, to the point where it's more of an example of Status Quo Is God (see below).
Sailor Earth: Ok, so Rudd used a star instead of a planet - the trope still fits.
Schedule Slip: for all of the usual reasons (real life,writer's block} plus at least one unusual one (deployment to Afganistan.) The schedule picked back up after the author announced that the comic was ending with Chapter Ten, perhaps because he now has a definite ending he's writing towards.
"There is a theory which states that if ever anyone discovers exactly what the Universe is for and why it is here, it will instantly disappear and be replaced by something even more bizarre and inexplicable. There is another which states this has already happened."
The girl who talks to Bay at the guys-turned-girls support group in the second prequel strip is Jo Starr from Cheer! and The Wotch
Stable Time Loop: Chris the producer created several by passing notes between his present and future selves through the time portal. Berry (an alternate future version of Bay), underwent several of the loops exploring The Multiverse until she nightsided herself by passing Chris a note that convinced him to destroy the portal in the past, saving our Bay but stranding herself in our present.
Talking Animal - Bay and Honey's cats. Of the two, Teri is usually much more talkative (and active) than Ams. They are also the same cat from different times, Ams being Teri's grown-up form from the future.
And Turt, a 76-year old turtle who Bay sometimes visits to try and help her find acting jobs.
And lately, a white female cat named Cleo, who Ams has a thing for.
Made explicit when it's revealed that someone can only be safely changed back by the same TF gun used to transform them in the first place, and as the gun used on Bay was malfunctioning it would be too dangerous to use it on her again.
Timey-Wimey Ball: from all of the mucking about in the timestream. Chapter 9 is even named "Timey Wimey"
Trauma-Induced Amnesia - In chapter 8 Bay lost several years of her memories after being hit in the head by a collapsing roof and forgot her Gender Bender as a result. Her reaction, and those of several other characters, allows the author to answer many questions without resorting to exposition.