Receipt for manual registration - HTML
I agree that this should be possible in the manual registration.
However, you could likely work around this using CiviRules. Not knowing your exact situation I'm guessing here, but this is how I might approach it.

Install the 'Email API' extension (needed to be able to send email from CiviRules).
Install the 'CiviRules' extension.
Create a new participant status simply so it can be seen by the rules engine. Maybe something like 'Registered (manual)'.
Create a new rule 'send email to manual registrants'.
Make the rule trigger 'Event Participant is added'.
Add a linked condition to the rule 'Participant status is (not) one of'.
Set the condition operator to 'is one of'.
Choose the new participant status you created 'Registered (manual)'.
Add an Action 'Send Email'
In this example, you shouldn't need a delay, but it can be useful to introduce a short delay to allow tables to be updated if you need to test them or get data from them.
Lastly, set the email parameters including the message template. You can CC, BCC etc.
Save and test with a manual registration for a fake user. You will have to choose you the custom status you created so the rule will trigger.

You could add an additional action to the rule that changed the participant status to the normal one after the email is sent.