First off, search engines (particularly Google) do a good job of resolving this issue for you. If I search for kuber or ku ber I get similar results. Searching for ku ber (with a space) also returns many results containing just kuber (no space).
Search engines discontinued use of meta keywords
Yes, the keywords meta tag plays no part whatsoever in mainstream search.
Only options are title, focus keyword and meta description.
Whilst the description meta tag can appear in the SERPS, its not actually used for search itself. So using keywords in this tag will not help you.
As far as I know, the "focus keyword" that YOAST reports is just a tool to help you target your content - it doesn't actually play a part in search itself.
The <title> is certainly useful to target keywords. As is the content of your pages. If you want to explicitly target both "kuber" and "ku ber" then both should appear in your content somewhere. However, you need to also be consistent - otherwise you just confuse your users. So, you can't just switch between "kuber" and "ku ber" in the same context as that just looks like a typo.
You need to focus on one version (I suspect "kuber" since that is the registered company name) and perhaps explain elsewhere (eg. on the "about" page) how the name came about with some background. There you can include "ku ber", etc.
but the domain name is "ku-ber.com" to further add to the confusion.
Yes, that does add to the confusion! The domain name itself does not help so much in search.
