RAW: we don't know. "Transformed" isn't a defined term, so we have to infer meaning from context. In the Slaadi context I infer a complete transformation that includes mental stats, abilities, personality, alignment, &c.
As "transform" isn't defined, we've got to look at its uses. Many times in the core set it's used in a context that has no bearing: an arrow transformed into a bolt of lightning, or the transformation described in Wind Walk. Following is a taxonomy of the uses of the term "transform" in the core rulebooks, as applied to characters and creatures with stats/abilities.
Some transformations explicitly do not affect mental abilities, skills, personality, alignment, &c.: druids' wild shape (PHB 66), Shapechange (PHB 275), killing a beast in the Beastlands (DMG 60, optional rule), Cloak of the Bat (DMG 159).
Some transformations change some, but not all of these brain-descriptors: Polymorph and True Polymorph (PHB 266 & 283, change mental stats but not alignment, personality), PC turning into a vampire (MM 296, mental stats don't change, alignment does, and player might even cede control of character to GM—personality change!).
Most transformations, though, don't go into detail: paladins' elder champion and avenging angel (PHB 87 & 88), Animal Shapes (PHB 213), and all of the shapechangers in the MM (doppelganger, lycanthropes, mimic, slaadi, &c.).
(Many more MM entries mention "transformation" in their flavor text, but that's usually in a description of how the monster/race originated, not an action that they take.)
So what about the Slaadi?
The transformation described doesn't specify, but we do have an important bit of context:
Slaadi reproduce by... infecting [humanoids] with a transformative disease called chaos phage.... [By this mechanism] blue slaadi spawn red and green (MM 274).
In context, it must be read that a humanoid succumbing to chaos phage is, in all ways, a slaad.
The only comparable we might have is the Vile Transformation of larva in Hades (DMG 63), which are said to retain "a few faint memories" of their time as humanoids. But there is nothing to indicate that a victim of chaos phage retains even that much.
Spoilers below!
(I have only played the adventure, but did not read it, so I might have missed quite a few encounters, distorting my impressions)
The enemy types are quite evenly distributed:
1. Humanoids mostly, as lycantropes also fall into this category
2. Undeads close second
3. Beasts mostly wolves and bat swarms
4. Fiends far behind the others
5. Fey even fewer
In Strahd's castle Humanoids fall to the third place.
Best Answer
There's no contradiction here. The Myconid Sovereign can only target corpses of Large or smaller humanoids and beasts with their ability.
However, a DM might choose to apply the Spore Servant Template to another corpse. As long as it is Large or smaller and isn't a construct, plant, etc., the template can be applied even if the creature isn't a humanoid or beast.
Just because the action to animate such a corpse isn't in the Myconid Sovereign's stat block doesn't mean that such a creature can't exist. Perhaps infecting a corpse of a non-humanoid/beast doesn't come up often enough in play to merit a mention here. Note that the monster manual doesn't describe the origin of every monster, or list every possible action every creature can attempt, just what's needed in a normal combat encounter.
The DM is free to apply the template to any creature meeting the requirements, and in the lore text you quoted, "A Spore Servant is a Large or smaller creature brought back to life by the animating spores of a Myconid Sovereign" (emphasis mine). Note the lowercase "animating spores"; this refers to the spores in fiction rather than the mechanical action in the stat block. It doesn't say "... brought back to life by the Animating Spores action of a Myconid Sovereign."