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. The 5% covers that, along with the website, the hosting and the push infrastructure behind the alerts.
It is a percentage rather than a monthly bill because the platform is only worth paying for once your ordering is busy, and that takes a season. In a quiet month you pay almost nothing.
It is per shop, not per staff member: put the app on every phone behind the counter at no extra cost. And 5% is a long way from the close to 30% a marketplace takes, which is the point of taking orders on your own site.