Yes , you did good by providing cover letter for this and supporting document to fill gap of ref letter.
I also have not submitted Ref letter but my eligibility recommended passed (confirmed from GCMS note)
One major document in this situation is rejection mail/letter from your HR/manager stating according to company policy they can not issue ref letter.
In my case this letter played major part as VO clearly mentioned in note "PA employer don't provide Ref letter, so he can not submit , refusal mail printput from HR atatched with application " recommended passed
Hope this will help you
Good Luck