As a sort of call-back to Super Paper Mario, the opening scene of The Thousand-Year Door remake features portraits of Mario's partners from Paper Mario. At the end of the game, Spoiler:a new second portrait of the partners from The Thousand-Year Door can be seen alongside it, lining up with the beginning of Super Paper Mario.

Both the original GameCube release and the Nintendo Switch remake are rated E by the Entertainment Software Ratings Board (ESRB), but the GameCube version's rating was simply given the descriptor "Mild Cartoon Violence". The remake’s ESRB rating was updated to replace it with the descriptors "Mild Fantasy Violence" and "Mild Suggestive Themes". These "Mild Suggestive Themes" most likely refer to flirtatious dialogue (i.e. "Aren’t you a fine specimen of a man"; "Perhaps if I…grabbed you and gave you a little sugar") and a character with a large chest/exaggerated proportions, referencing Madame Flurrie.

Whacka has an entry in the enemy name table and a tattle. Based on the tattle, it seems that earlier in development, instead of disappearing after being hit enough times, he would attack.

This concept was eventually implemented for the Nintendo Switch remake of Paper Mario: The Thousand-Year Door. Spoiler:If Mario hits Whacka at Keelhaul Key until he flees and revisits the Pit of 100 Trials after defeating Bonetail, Whacka will appear as an optional superboss on the final floor. True to his unused tattle in the N64 game, Mario must hit him in order to begin the fight.

Within the GameCube version's data are graphics for an earlier Vivian design depicting her with a shorter body and a flame on the tip of her hat. Concept art included in the Nintendo Switch remake reveals that the latter trait was part of an early design for all three Shadow Sirens, with Beldam and Marilyn also having a shard of ice and a lightning bolt at the end of their respective hats. This concept art additionally depicts the Shadow Sirens with black skin, which was changed to purple by the time the early Vivian sprite was created.

The gender identity of the party member Vivian is inconsistent between different language translations of the original game. In the Japanese version, Vivian identifies and presents as female, but is described by other characters in the game as actually being an effeminate-looking male, aligning with common media depictions of transgender or gender non-conforming characters at the time, but not explicitly referring to Vivian as such. A rough translation of the Japanese text for Vivian as a party member reads:


The French version directly carries this over and additionally describes Vivian as a boy pretending to be a girl, while the Spanish version describes Vivian as a boy who looks like a girl. However, according to former Nintendo of Europe translator Pol Roca, Vivian's Spanish name "Bibiana" was intended to be a reference to the Spanish transgender actress Bibiana Fernández, who starred in the 1977 film Cambio de Sexo (or Sex Change).

The English and German versions remove any references to being transgender or gender non-conforming, implicitly portraying Vivian as a cisgender woman with "a bit of an inferiority complex". Instead of being bullied over her biological sex, her sisters instead belittle her for her appearance.

The Italian version of the game on the other hand explicitly depicts Vivian as an openly proud transgender woman, with the localization reconfiguring her relationships with gender identity and her sisters by having Marilyn and Bedlam's bullying being rooted in jealousy, traits which are absent in the Japanese script:


The English release of the Nintendo Switch remake follows the Italian version of the original game in unambiguously describing Vivian as a transgender woman, most prominently featuring a line where Vivian states that "it took me a while to realize that I was [Marilyn and Beldam's] sister... not their brother." It's currently unknown if Vivian's portrayal in other translations of the remake has changed from the original release.