I'm planning to root my Samsung device (Galaxy S6 Duos) and it can and will trip KNOX which disables Samsung pay. What's unique with Samsung pay is that it can use Magnetic Secure Transmission (MST). It allows the phone to broadcast data by simulating a magnet/magnetic strip.
Now, I'd still like to utilize the hardware after rooting. It would be a waste to have MST hardware but no software.
I've done quite a bit of research about it but what turned up is mostly just explaining what MST is and why Samsung has bragging rights about it.
Is there an SDK I'm not aware of that lets me use MST in a Java app?
If there is such an SDK, Samsung (or whoever) is keeping quiet about it. I can't find anything using Google. (As suggested in a comment, you could ask Samsung directly on this.)
Here's why I think you won't be able to obtain a (free) SDK.
Samsung seems to have a reputation for not being "open". (See various comments on android forums.)
MST is based on patented technology. Samsung bought the patent for (presumably) non-trivial amounts of money.
We can assume that Samsung >intends< to make money from the patent by either using it as the "killer" advantage for all new Samsung phones, or licensing it to other phone manufacturers.
Giving out an SDK as a free download would run counter to the above goals. If 3rd-party developers can embed MST in non-Samsung phones, or in old Samsung phones, that undermines the (inferred) business model.
Even if it didn't undermine Samsung's business model, an SDK offers minimal advantages to them1. You think they want to help out people who have "rooted" their Samsung phones? Doubt it!
1 - Clearly, that is debatable. However, I'm trying to represent the mindset of the current Samsung management who would need to decide to commit resources to make their internal MST codebase into a freely downloadable SDK. See also, the first bullet ...