After updating to 2.1.7 when create/edit feature box category/item I can chose only core templates, even I have custom on /my_theme/templates/featurebox/
Check it with landingzero theme - same
I confirm this issue. This list ignores theme template array. Field type "layouts" ;

This change fixed this inf form_handler.php:

This commit: https://github.com/e107inc/e107/commit/229f0486aa13fc1f6d6f5350c45ad9fb5930cd1b
e107_plugins/featurebox/admin_config.php
'fb_category_template' => array('title'=> FBLAN_30, 'type' => 'layouts', 'inline'=>true, 'data' => 'str', 'width' => 'auto', 'thclass' => 'left', 'writeParms' => 'plugin=featurebox&id=featurebox_category&merge=1', 'filter' => true),
to:
'fb_category_template' => array('title'=> FBLAN_30, 'type' => 'layouts', 'inline'=>true, 'data' => 'str', 'width' => 'auto', 'thclass' => 'left', 'writeParms' => 'plugin=featurebox&id=featurebox_category&merge=0', 'filter' => true),
merge=0
This is perferct. This way it includes only theme templates.

@CaMer0n With solving this issue could you consider set it as merge = 0?
If theme doesn't have featurebox templates, plugin templates are displayed.
If theme has FB templates, you normally copy plugin file in theme folder and then you let there what you want in theme.
Or set this in FB plugin preferencies (better maybe because existing themes)
@Jimmi08 Please try with my changes. merge is currently set to true by default. But we can change it if you guys think it's better to be false by default.
this works for feature box category