Transporting individual business functions

I have observed a few discussions on this topic, but was hoping to start a new as the others had some other moving parts (industry solutions/etc).

We have a couple of projects going on in a DEV environment that require a number of BFs to be activated. The are in the FI, HCM and LOG areas.

One of those projects would like to move the QAS system but it seems the transport option in SFW5 will move all that have been activated.

1. It seems the only option is to activate manually in QAS (and PRD) despite that being against recommendations?
2. Are there potentially going to be issues if we don't activate BFs in the same order? I hope not, as this would seem like a very limiting design approach from SAP!

Thanks for any input!!

Eric