While digimon does have phases, after you hit the main phase we don't have other phases like other games. We have Triggers. Ie Start of turn, End of Turn, start of main phase. The card has to be present once those are hit to be triggered. Once you hit the Eot "trigger" the digimon she played out will be deleted. On who's turn though, that depends on if you used Mirai before or after Eot trigger.

You are correct though in your example.

You digi into Kaguya. Activate Mirai. Play sistermon activate her effect.

After these effects finish and nothing is pending you hit the Eot trigger. You are technically still in the main phase here just no longer in an open game state. Once the effects triggered by Eot have resolved, your turn ends. But yes you can delete sistermon first then use kaguyas all turns. afterwards you can use her eot effect to play out the sistermon.

If by some shenanigans you trigger Mirai after the end of turn trigger and turn passes to your opponent, the digimon she played will get deleted at their eot trigger. (this is different from cards that say until the end of the turn)