Changing production code is usually done due to two reasons:

1. Optimization - All mobile A/B testing platforms. (Manually or automatic) - http://www.appiterate.com,http://www.leanPlum.com,http://www... http://www.useartisan.com)

2. Quality issues - Either technical or UI Here there as far as I know one unique company http://www.rollout.io that gives developers control over their production environment from hard core bugs hot-patching and UI changes to SDK control and analytic control.

I'm guessing all of these companies use the same technology which seems legit in regards to Apple, as long as none of them are using code injection.