How to make Karabiner work with Intellij on Mac?

I’ve recently switched from Windows/Ubuntu to MacOS Catalina and I’m trying to avoid changing too many key mappings on Intellij 2020.2.

I’m trying to achieve these things:

1. Swap Left Ctrl and Fn
2. Having function keys as default in touch bar when using Intellij to be able to use combinations like Ctrl + F4 in Intellij without having to press any additional (Fn) keys
3. (If possible) Map Ctrl + click to something other than Right Click

Here’s what I’ve done so far:

1. Swap Left Ctrl and Fn using Karabiner
2. System Preferences > Keyboard > Shortcuts > Function Keys > Add Intellij
3. Imported a complex modification in Karabiner to change Ctrl + click to just click.

The issues that I’m facing:

1. Pressing original Fn (mapped to Left Ctrl) in Intellij changes touch bar from Function keys to other touch bar options. I’d like to disable this to be able to use Ctrl+F4.
2. Left Ctrl+Click still behaves as right click.