Yes, if your ‘ducer is not pointing along the long axis of the boat, it will affect your unit’s performance.
It’s hard for me to help without seeing your boat and the dimensions of that step. Are you running a jack plate? A lot of bass boat installs that I’ve seen have a custom bracket made to hang off the jack plate. That keeps the SI ducer in the water when motoring at slow speed, but out of the water on plane. You’d need a second, through hull ‘ducer for high speed operation.
The guys at Skeeter Boat Center have done a bunch of these. Their install rates are very reasonable, and the service is fast! Consider contacting them to get your unit rigged professionally.