If I use other mods that allow some blocks to be a part of protal frame (Example: crying obsidian and obsidian glass in Better nether mod), then protals cannot be created with these block.

I want to add( not sure if it's 100% the reason it happens) that the recent Create 0.5 trains do not work with it because of this.

This is hard to fix as it's very hard to automatically detect which block that another mod allow to use for nether portal. But it can be configured by custom portal generation https://qouteall.fun/immptl/wiki/Datapack-Based-Custom-Portal-Generation.html

@Defalting You can configure it manually https://qouteall.fun/immptl/wiki/Datapack-Based-Custom-Portal-Generation.html

Thank you @qouteall