By default WordPress sanitizes the slugs (post names) with
sanitize_title() function. The dots, accents and other non-standard character are automatically removed from native slugs, when the post is saved or updated.
Permalink Manager overwrites the native permalink system and allows to bypass this issue.
Adjust sanitize settings in Permalink Manager options panel
It is also possible to keep the dots inside the new permalinks when the post, page, CPT item or term is created. All you need to do is disable “Strip special characters from slugs” option in Permalink Manager settings and “Use actual post/term titles“. After the new settings are saved, Permalink Manager will use the post/term title instead of the native slug.
When this option is active, Permalink Manager will not use the native slug (where the dots are replaced with hyphens) but will use custom slug inside the new default permalink (the dots will not be removed).
How to keep the dots in old permalinks
If you would like to keep the dots inside the permalinks of already added posts and terms, you will need to either regenerate custom permalinks or change the custom URIs and add them again manually.