At present Runloop only offers apps that are either paid for upfront or contain non-consumable in-app purchases. You will only ever be charged one time.
Apple App Store
Apple will not charge a user for the same paid app, or non-consumable in-app purchase twice as long as they are using the same Apple ID that made the original purchase. Instead they will advise the user that have already purchase the product and offer for them to download it again for free.
There are a couple of situations where it is possible to be charged twice. Though technically you are not being charged twice for the same product.
Seconds and Seconds Pro
For legacy reasons Seconds comes in two variants. There is Seconds Interval Timer and Seconds Pro. Seconds Interval Timer comes with an in-app purchase to upgrade, Seconds Pro is a paid app.
Although the two apps are exactly the same once paid for, they are not considered the same product by Apple. That means that it is actually possible to purchase both versions of the app. If you find yourself in this situation you should contact Apple for a refund.
Different App Store accounts
Purchases cannot be transferred across App Store accounts. This means you cannot transfer your purchase from one Apple ID to another, or from an Apple ID to a Google Play account (of vice versa).
In this case, it's simply two different users purchasing the same app.
Checking your Purchase History
To confirm that you have only purchased a product the once with the same App Store account, you can check your Purchase History.