Airmail now allows you to create signatures in iPhone which are restricted to the Airmail for iPhone app only. This too, can be customized per account, which means you can do this for the custom number of accounts from your list or all of them.
To achieve this behaviour, please follow the steps as explained below.
Firstly, go to Airmail Settings as shown in the picture below.
Then choose iCloud from the list as shown in the picture below.
Then choose the account from the list for which you want to create signatures and not sync them over iCloud. This is shown in the picture below.
Then choose the required option as shown in the picture below.