Another option is to create a default email address for each domain under the account so if you have DomainA.com and DomainB.com in the account, create [email protected] and [email protected]. Then create the aliases under those two users. That way if you forget to change the FROM field, at least the email comes from the same domain. While it costs an extra $5 a month for the added user, it is a safeguard if you are concerned about forgetting.
The other benefit is that Google surprisingly has decent phone support for Apps for Business. I have had a couple issues over the years and a quick call got them resolved quickly. There is typically no wait time and you speak directly with a support person. Not really a deal breaker, but it is an added plus when evaluating products.
What does the process look like when you're changing the FROM field when composing an email (e.g. sending from [email protected] and then another email from [email protected])? I'd hate to forget to change it and send out an email from the wrong email address. But it would be nice to manage all emails from one account.