The reason why the customer count in the app may be lower than the total number of customers shown in the Shopify admin is that Loyal does not analyze all orders for segmentation purposes but only those meeting certain conditions. Loyal only imports data from those orders where the order:
has a customer ID,
has not been canceled,
has been paid, partially paid, or partially refunded,
is not a test order,
has been placed within the last ten years from the time of importing/syncing.
The main purpose is to consider only "real" orders from actual customers for the analysis. For this reason, some customers from Shopify may not be included in the segmentation (e.g. a customer who placed an order but has not paid for it).