Does Touhou Project actually have yuri canonically? I'm pretty sure it's all from the doujin, it's more "squint really hard during the few moments of interactions between bullet hell" kind of thing. GrimGrimoire definitely requires less squinting, it's pretty easy to see the yuri moments in that game.
Some Atelier games have some yuri if you focus on their interactions. Summon Night 5 is an srpg that has a legitimate non-subtext yuri route with your kouhai and a summon/cross in the game refers to you as onee-sama and is very affectionate with FeMC too. Summon Night Swordcraft story (and its sequel) has a lot of blatant yuri content, especially if you pick the female summon.
Fate/Extra and Fate/Extra CCC has so many since the script/dialogue/every written word is exactly the same between female and male protagonist - so every female character that develops any kind of attraction to the protagonist does so regardless of gender; not to mention it's specifically mentioned that they're bisexual, so it's intentional. Another result from the same script is that FeMC shows attraction to female characters + I actually haven't encountered a single moment where she's attracted to male characters, so it's pretty much impossible to play a straight FeMC in these games. In short, the script is so very obviously written with a heterosexual male protagonist in mind, but since they basically copy and pasted the same script for the female protagonist, it becomes incredibly gay while also inadvertently creating a really strong female protagonist. Top recommendation for these jrpgs in terms of yuri.