Solution

I too had the same issue where the invoice email's body content was Center Justified instead of Left Justified. The QB online chat person helped me to fix this today, as well as to set the Left Justification as my default for all new (not prior) invoices. These are the steps I took on a Macbook. 

Step 1 - Open a new blank invoice

Step 2 - On the new invoice, select Manage (gear icon), and the side pane will slide open (if not already open). 

Step 3 - In the slide out pane, select Design

My template was set to Modern, with default also set to Modern

Step 4 - Select Standard

Step 5 - to the side of Modern, click on REMOVE DEFAULT

Now, future invoices, starting with this one, will be set to the Standard layout (left justified text). As an added bonus, this new Standard setup also gets rid of a gray frame which surrounded the white email text field. This was only seen by the recipient, and it didn't look great. The formerly gray boarder is now replaced by white, so it is seamless between the email body text field and the boarder (same whites). 

Hope this helps other QBO users. The fix was not intuitive at all. I had created new templates, edited text fields, and nothing worked until changing the default, as found on the invoice page.