WebApp not inheriting Safari Settings

I have a simple web app that launches Safari (full screen mode) calling a website (let's call it website A) containing another website (website B) in an iframe. Website B uses cookies. When i launch the app, and the window opens, website B fails because the cookies aren't being set. Looks like Website B is considered a third party website because its contained within an iframe.
If i call website A outside the web app, both websites work fine.
I found that enabling the Safari cookies option to always allow third party cookies determines whether website B works in Safari, but it has no bearing on it when i call it from the web app.
Why doesn't the web app inherit the safari settings? Is there any workaround or setting that i've missed?
Device: IPAD with ios8
Thanks in advance.

Basically web start can only pick up the settings of whatever
happens to be the current Windows default browser. If that's Netscape then the Netscape settings will be used.
Since your clients are using a script to specify the proxy settings you should also be aware that there's an issue with web start 1.0_01 where it locates the proxy setting based on the first occurrence of the word "Proxy" in that script. This can cause issues if the first proxy
listed is for https only of even if the first occurrence of "proxy" is
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