I am not sure what effect CMT will have on the final weld as regards post weld strength, although I would imagine it would be beneficial compared to more prevalent welding processes. I would suggest you allow the weld to age after welding.

From memory, you will never achieve anywhere near the tensile strength of T-6 without heat treatment after welding. PWHT is nearly always possible with consideration to jigs etc. If not, then I would question the use of T-6 material. 

4043 or 5356 are the fillers of choice, 5356 has a higher ductility, 4043 has lower shear strength....

Typically the loss of strength in the weld and heat affected zone are taken into consideration by the design engineer and the weld size and base metal thickness are factored with these considerations in mind.

There are heat treatable filler metals available, but even those will not return original T6 conditioning.

The CMT (cold metal transfer) (if used properly) will have the advantage of a smaller heat affected zone and lower total heat input for a given travel speed.  How exactly does the CMT affect the zone?  That would be an engineering level calculation that came after PQR information had been acquired.

CMT is typically used on aluminum materials thinner than 16ga. or  .063.   It allows for excellent fillets on aluminum thicknesses that previously could not be welded with GMAW..........  For aluminum materials above 3/32" thickness, I see no use for CMT

Edit:
This is a good, free "beginning" piece to read about aluminum joining, for those who are interested
http://www.maxal.com/files/QuickSiteImages/Maxal_Guide_for_Aluminum_Wldg_6-11_doc.pdf