I have been wondering how to obtain the bottom and top versions of sex scenes in this game, but I just can't find the answer to it. Can someone tell me how to be either a bottom or top?

Getting bottom: Use flirt to fill the enemies lust meter between 40-90%. Lose the fight by Lust or getting beaten up. Not 100% garantied

Top/choice: Win the battle by filling the enemies lust >100%. Does not work on all enemies.

I was also wondering how to do it with NPCS because I saw different sex scenes with Axel. But I am not sure since I was trying to figure it out myself.

Whether sex scenes include the main character being bottom or top is determined by the prescripted events. Note that there are third-party game guides available that explain the requirements for obtaining certain sex scenes:

• GALLERY - FANMADE_GUIDE by Redyoshi
• 【Tavern of Spear矛之酒館】CG解鎖、地下城副本、支線小任務攻略詳解(22/12/9再更新版本) - persis33的創作 - 巴哈姆特
  In Chinese(Taiwan)
• 【CG】矛之酒馆C/G画廊解锁指南（至0.23） - 哔哩哔哩
  In Chinese(China)

Also, note that there’s no guarantee that a particular position sex scene will be available with a specific character in a specific plot route, future updates may change this, though.