I decided to equalize the header on the main site and on the Flarum forum, and copy-pasted HTML/CSS/JS for header menu from the website to the Custom header.
This code contains import of bootstrap4 minimized CSS file. As soon as it's included forum UI is messed up in a few places (I don't think I explored all the broken/misaligned parts, reverted it immediately as there is no way to safely test it).
The question is – is a known issue or I'm doing something wrong? I believe custom header is not that rare use case, and many headers contain bootstrap/jquery for menus and for handling responsive menus. So my guess is that is should be known issue.
And advice how to deal with such a problem?
PS. I run Flarum beta8.