Companies writing applications for Apple’s iPhone remain confused about whether their solutions run afoul of Apple’s terms, or whether it will even enforce them, according to third-party development organizations.

Apple updated its iPhone Developer Program License Agreement in June to give developers the option to embed integrated code into their applications, but in a limited way and only with Apple’s prior written consent.

The uncertainty remains in spite of the June license changes, according to Unity CEO and cofounder David Helgason. “The honest answer is that there is no clarity, and I’m not aware of anyone who is in possession of clarity,” he explained.

“When [the terms] were announced as a plan three months ago, clearly it said that a large section of games on the iPhone wouldn’t be allowed under those terms.”

In April, Apple modified the license to ban cross-compiled applications from its App Store. Apple specified that the iPhone SDK’s APIs must be used in the manner prescribed by Apple, and they cannot call private APIs.

Adobe’s Flash-to-iPhone cross-compiler, which is included in its Flash Professional CS5 release, was forbidden by the licensing terms.

The license also specified that iPhone applications must be originally written in C, C++, JavaScript or Objective-C. That left tools (including Novell’s MonoTouch, which brings .NET development to the iPhone, as well as Unity’s Unity 3D game authoring tool) in a state of uncertainty.

In the interim, Apple gave an indication that the terms may change or that it may not actually follow those rules or enforce them, Helgason added. “The updated terms,” he said, “grant permission in certain circumstances, but I’m not aware of anyone having that permission.”