Hi Joel,
The answer is that there are some differences but for the most part the BCC offerings for the FCP and AE host applications are the same. Here’s a list of some of the major differences:
In FCP, there are “RT” versions of many of the filters. The RT version does not include the built-in motion tracker, which is removed so that the filter will playback in the FCP timeline without the need to render the sequence. The RT filters are not included in the AE version as the AE version will preview without the need to render to disc.
In FCP there are “real” transitions, which can exist between a pair of clips and therefore there is an entire category of FCP Transitions effects. In AE this is not possible and transitions are treated just like any other filter effect.
I think that depending on the type of work you are engaged in that you will still need to use both programs. If possible, I would suggest that you upgrade both hosts, FCP and AE, to the latest versions and equip both hosts with BCC 7. This will provide you with the toolset that you need to handle most motion graphics, editing or compositing work that will come your way.
And if you need to transfer an edited sequence from FCP into AE you can do that with Boris XML Transfer, which is the only timeline transfer utility that will transfer BCC filters between hosts.
I hope this helps.
Cheers,
Peter.