Can 2.4GHz antenna radiate through a small enough enclosure opening?
I've dealt with RF for about 10-12 years now, and my best recommendation is to spring for the extra $$ and use the antenna mounted to the top PCB.  Putting the radiating element under another layer of copper, silicone, and other materials will attenuate the signal by (very exact answer here) a lot.  On the other hand, if you plan on using the Bluetooth interface in very close proximity (less than a meter), it may not matter much.  You could always build a prototype of each one and use a spectrum analyzer to measure the performance before putting your design into production.  Also, if the whole thing is going to be encased in metal, the BT antenna mounted to the top PCB will probably be severely attenuated as well.  You may want to consider a material with better RF transparency for the case.  Plastic, maybe?