There are two questions in your question:
1) can I use a system other than IAP to allow users to make purchases?
2) if I can, can I use that system within the app.
The answer to #1 depends on what you are selling. Apple requires the use of IAP for use of code that they distribute but not for real world goods sold using an app that they distribute. This is explained in the guidelines with an interesting exception in 11.14.
If the use of a non-IAP system is allowed, then the answer to whether that system can be imbedded in the app depends on how Apple is interpreting 11.2. One way it can be interpreted is that you can't have that "system" "in an App". This interpretation is supported by the requirements in 11.14. But another way to interpret 11.2 is that the "system" can be in the app, just the stuff bought ("content, functionality, or services") can't be used in the app. Here is the ambiguous 11.2:
11.2 Apps utilizing a system other than the In-App Purchase API (IAP) to purchase content, functionality, or services in an App will be rejected
So it is unclear whether you can imbed a system other than IAP into an app for purchases of real world goods and services. But clarity to that question is clearly not obtained through the argument "they did it why can't I".