I have all Alpine DDrive components. Great speakers and I've had them for many years.
The rear speakers are actually 4". I somehow squeezed in 5 1/4. You have to modify the plastic housing a little in the door panel. There is a ridge on the rear mounting surface which prevents just any 5 1/4 speaker from fitting flush against the surface. The factory speakers are not your run-of-the-mill auto speakers and were obviously designed with the abnormal surface in mind.
However, most aftermarket speakers don't take such things into account. The front wasn't so bad, but I still had to use silicone sealant to be sure that there was no air between the speakers and the plastic mounting surface. I think Toyota wanted to make it difficult to replace the factory speakers. Of course, you could just make your own custom mounting surface.
The 5 1/4's I installed were separates and here is where I mounted the tweeter and painted to match:
Now, if you want to go for a BIGGER speaker, I did help a friend install JBL 6.5's in the rear.
To do this we took the OEM 4" plastic mount and used it as a template against a sheet of 3/8" MDF. We also glued-n-screwed a short piece of PVC conduit on the front and back of the MDF as a mounting standoff similar to the OEM bracket. With a little foam weatherstripping and black paint it looks factory. There was very minor plastic trimming necessary to the backside of the doorpanel. No a big deal. We then flush mounted tweeters in the C-pillar plastic trim above and behind the passenger's heads aiming and crossing forward. The external crossovers were easily mounted behind the plastic trim.
The installation took a while, but it looks very nice and the imaging is very good. I would recommend to anyone doing a speaker upgrade to look at separates w/ the tweeter located up higher.