An app on the Play Store is not a thing you build once. Google changes its target-API requirement every year, the permissions rules move, and a listing that stops meeting them stops being installable, so the app needs looking after for as long as you want it on your staff's phones. That is what the $49 covers, along with the push infrastructure behind the alerts.
It is free for the first twelve months because the app is only useful once your ordering site is busy, and that takes a season. You will know whether it earns $49 long before you are asked for it.
It is per shop, not per staff member. Put it on every phone behind the counter at no extra cost. There is no per-order fee and no percentage of sales, which is the entire point of taking orders on your own site rather than through a marketplace.