As for your question "FlashInApp can only be used in 32 bit applications", yes, one cannot create a screen-saver for 64 bit Mac using FlashInApp framework, FlashInApp can only be used in 32 bit applications.
Flash'In'App supports both 32-bit and 64-bit versions of main operating systems. Currently, this support is based on 64-bit platform's capability to run 32-bit applications. So with Flash'In'App you can develop only 32-bit applications that use the 32-bit version of Adobe Flash Player plugin. Your 32-bit application, developed with Flash'In'App, will run on both 32-bit and 64-bit operating systems. This is not our limitation, however. It happens because there is still no 64-bit version of Adobe Flash Player plugin for Mac OS X. Our development team is currently working on resolving this issue asap though.