Start by deciding, in writing, which system owns which metric. Revenue, orders, average order value, refund rate, repeat purchase rate and product performance come from the store. Sessions, channel share, landing page behaviour, funnel drop-off and device splits come from GA4. Every dashboard then cites its source next to the number, which ends most reporting arguments before they start.
Next, make the tracking as durable as is reasonable. A proper data layer, consistent ecommerce events through checkout, consent handling that reflects the regions you sell to, and a server-side path where it is justified all reduce the drift without pretending it disappears.
Finally, connect them where it matters for decisions. Pulling both into one warehouse or a single reporting layer lets you put channel behaviour beside real order value and customer history, so acquisition decisions rest on margin and repeat rate rather than on session counts alone.