Does not matter how many flees you can stack on the head of a pin, when the plan is to toss the pin anyway.
As to 1st ??? No benefit performance or sound quality advantage to having all the components from the same brand. Brands? Kicker, Wet Sounds, Clarion, Fusion, Aquatic AV, Rockford, JL Audio all make solid units with various features. Some are traditional single DIM, some have over sized faces. Some are gauge style and others are more square or rectangle.
#2 A 4 chnl will easily drive 3 pair of in-boats. Perfect for one bow pair and 2 main cabin pair. A 6 chnl will also work great. For future additions, I would suggest a 5 or 6 chnl amp and consider a mild woofer to round out the in-boats sound quality. With amplified in-boats and the addition of a 3rd pair, the added bass will be great. As to future tower speakers, I would suggest a separate amp for them, once the time comes. There are some 6 and 8 chnl amps that can work to power in-boats and towers, but you really need to have a very specific plan in place. So if you are not sure about what those future tower speakers will be, leave that for then.
#3 proper in-boat? Once that fits, fits the budget, you like the look and sound of. Go with a quality built marine speaker.
#4 yes
#5 Depending on use, there is certainly going to be an increase in amperage draw. If the boat does not already have a dual bank setup, id factor that into the plan.