other games beside vertical flagged games seem to work in vs cocktail mode like bubble bobble and metal slug.
Yes,
most horizontal games will work like Bubble Bobble with players seated to the left and right of this screenshot.


I am having trouble with a few games where in cocktail mode the image is side by side as if my screen was being used horizontally from the top and the bottom. I've tried rotating and cocktail mode and its still placing the images side by side instead of opposite facing screens for vertical play
For vertical games, most of the default layout files assume the players are seated at the top and bottom of this Space Fury screenshot.

To change the positioning/orientation of the screens, look into a mix of these options:
- Make custom .LAY (layout) files to change from side-by-side to head-to-head
- MAME Diipswitch menu settings
- MAME Video Options menu settings
- Mapping P1 and P2 controls to the P1 inputs in the MAME "Input (this Game)" menu-- for some games the upright cab used alternating gameplay with one set of controls and no screen flipping but the cocktail cab used two sets of controls and screen flipping.
Unfortunately there are no one-size-fits-all easy answers.
Every game needs to be checked/reconfigured.
If you do make some custom .LAY files please considering sharing them here and/or on Mr. Do's site like big10p did with his great widescreen layouts.

Seems like these "Vertical WS Cocktail" layout files would go
here in the "Other Artwork" section with a "WS" flag and maybe Mr. Do could add a "VC" flag for Vertical Cocktail.

Scott