Shizuku's license disallow 3rd party recompilation of the APK, fork or not. Presumably this is done to provide an option to legally takedown fake Shizuku which could contains backdoor. (The original APK is redistributable) Hence Shizuku is not on F-Droid.
F-Droid, however, allow the developer's binary to be reproduced if they have tested that the APK is reproducible when replacing the APK's signature with the original APK.
It allows recompilation, just not using the official logo. Similar to Firefox in Debian kind of issue.
Reproducible builds would allow distributing Shizuku in F-Droid, that’s correct. (If Shizuku banned third party builds by the means of code license, it would not be FOSS and thus wouldn’t be eligible for inclusion in F-Droid altogether.)
F-Droid, however, allow the developer's binary to be reproduced if they have tested that the APK is reproducible when replacing the APK's signature with the original APK.