Does if matter if our Government Gateway email address is different to the Company email address in QBO for when we turn on MTD within QB ?

Welcome to the Community, @sheila.bonney.

It doesn't matter if you have a different email address when turning on MTD. I'd be glad to share a few information about this.

Your Government Gateway email address receives emails from HMRC. While your company email address receives email from QuickBooks.

You can check out this article to learn more about MTD: Making Tax Digital (MTD) - FAQ.

Please know you can always get back into this post if you have more questions. I'll keep an eye out on your response.