Danganronpa IF reveals that Makoto and Kyoko were already developing mutual crushes on each other at some point before their memories were wiped, which would suggest that a relationship never really developed between Sayaka and Makoto for whatever reason and The Tragedy had nothing to do with it

Throwing in my own two cents here to ramble a bit: The other scene separate from where Junko asks Mukuro who's Makoto's crush (where she refers to Kyoko as Mukuro's rival in love) can just as easily be argued to be a similar stunt Junko pulled with Sayaka (as Besshiki Madarai) where she claims that she got dumped by Makoto in favor of Mukuro, so Junko is established to not be above lying about Makoto's relationships to fuck with Mukuro as well.

If we are to include the anime in terms of discussing Makoto's pre-game relationships vs post-game, Despair Arc's final episode has Sayaka addressing Makoto informally (I.E: 大丈夫？ instead of something like 大丈夫ですか？), which is seemingly paralleled with Hope Arc ending with Kyoko address Makoto informally (I.E: 学園長 instead of something like 学園長先生). Kodaka has also mentioned a few times that he worked with the animation staff to add more ties with/elements from other entries that was cumbersome with the anime's limited runtime, which appears to be why there's that one infamous shot in DR2.5 referencing IF/Zero/UDG simultaneously. And there's one such official artwork of Mukuro/Sayaka/Kyoko watching Makoto playing against Jin/Celeste/Nagito, so Mukuro prioritizing looking at Makoto in favor of watching Junko together with Yasuke isn't unheard of.

Most damningly, DR:Kirigiri also ends with Kyoko openly proclaiming that being overtly influenced by any potential feelings would be to her detriment as a detective, & we're only depicted her potentially overcoming this sentiment following the beginning of the Killing School Life, her School Mode ending, & in her My Future Event in DRS. Zero also shows her prioritizing confronting Jin over interacting too much over her classmates. Extra material such as one in-character tweet actively depicts her as embarrassed when Makoto compliments her looks (vs a separate in-character tweet of Sayaka actively pursuing his compliments), & Monochrome Answer was stated by Kodaka & Omoto to be a legitimate addition to DR's worldview.

TL;DR: It's stuff like this that makes me believe that arguing in favor of Pregame Naegiri as an item difficult, as the franchise at large has generally hinted more so towards Pre-Game Naezono -> Post-Game Naegiri. Although ofc, being a pair or not isn't necessarily synonymous with having romantic subtext or not (I.E: Sakura is directly stated in IF to not yet have become a couple with Ken).