“We are interested in creating a native app in android and ios that could capture in the native and publish to flash (for the browser based version). Is that possible?”

Flashphoner Web Call Server works as a SIP user agent.
It means it should be compatible with any SIP softphone including IOS and Android softphones.

So, you will have to use a mobile SIP SDK or customize any open-source Android or IOS softphone. For example IMS droid or proprietary softphone like Bria or PortGo which have branding and customized Android and IOS versions.
And you will be able to call from the mobile softphone to Flashphoner and establish audio/video call Flash-Sotphone for users of your video chat.
Flashphoner Web Call Server supports one-to-one SIP conversation. It does not support many-to-many SIP conference and need for intermediate conference SIP server for such case.