Because it's the only contact Toneri had with Hinata (the Last) - stands to reason, its the most probable way he was able to influence Boruto (eye)... from watching the anime, seems he planned it all out before Boruto was born... I'm not pointing at any specifics - jutsu or chakra - but they did spend time together before Naruto rescued Hinata... there is some aspect of speculations in the reasoning
Yeah. . .no. . .Toneri;'s long term plan was to have babies with HInata and perhaps Hanabi to repopulate the planet. . .whether they were willing participants or not(that Toneri forced Hinata into marriage sez everything right there).. . .Toneri suffered from 'Villain Decay' to the extreme
Any 'help' Toneri gives to Boruto should be accidental because of what he would've done to the sisters if he won.
Toneri was just another 'old school Orochimaru' who ended up suffering through villain decay along while getting a dose of Karma Houdini. Granted Hinata did painfully get her sister's eye back, there was no further punishment.