I'm having a near identical problem. I installed NodeBB a few weeks ago, started using Vanilla, then started customizing it via the admin custom HTML & CSS tools.
Then I started following the burnaftercompiling NodeBB theming guide to make my own theme. Everything was going well until I spun up NodeBB with my new theme. Everything looked very weird, like OP's image except my custom HTML/CSS and site-wide CSS files were loading.
I used ./nodebb dev and got similar errors about an inability to minify:
error: [meta/css] Could not minify LESS/CSS: variable @brand-primary is undefined
I recursively grepped from webroot and found @brand-primary defined in bootstrap/variables.less and set as "@brand-primary: darken(#428bca, 6.5%);"
This file is in the Vanilla theme directory, as it was imported inside theme.less, as per the instructions..
"./nodebb reset" threw an error, so I ran "./nodebb reset theme" and it re-set me to Vanilla from my custom theme.
Any thoughts? I'm burned out for the night. Also side note, what tags to I use to get the code format? Thanks.