minor success: I noticed the web server logs didn't include the total base URL for the template (
https://example.com/atom/ but the templates were being referenced by /dist/css/... instead of /atom/dist/css/...)
I manually edited
atom/config/unavailableB5.php
atom/config/error/errorB5.html.php
atom/plugins/arDominionB5Plugin/templates/_layout_start.php
And the shape of the template has been corrected, but now the background color for the menu section is inexplicably white, so the images are white-on-white.
Writing more as I fix things:
edited atom/apps/qubit/templates/_header.php to add bg-dark in the header:
diff _header.php /var/www/atom/apps/qubit/templates/_header.php
25c25
< <header id="top-bar" class="navbar navbar-expand-lg navbar-dark d-print-none" role="navigation" aria-label="<?php echo __('Main navigation'); ?>">
---
> <header id="top-bar" class="navbar navbar-expand-lg navbar-dark bg-dark d-print-none" role="navigation" aria-label="<?php echo __('Main navigation'); ?>">
and things now look normal. I don't remember having to do all that previously with 2.8. I assume there's a more global setting for including the base path, but the lack of a dark background for the white icons in the default theme seems like a bug.