Are there associated problems regarding portability?
Only if you continue to have "port-specific files".
Will it pay in long run?
Off-the shelf is cheaper than hand-built. Period. You should be very, very reluctant to hand-make anything. Always download first, rarely customize, and build new only when it's impossible to press an existing tool into service.
what should be my choice: "cmake", "scons" or some other?
It barely matters. You can toss a coin now.
You can download both and try both. They're pretty easy to learn.
After learning them, you can then toss a coin.
The important thing is to throw away your hand-made build system as quickly as you can. In order to do that you have to completely learn the new one. Many folks refuse to completely learn the new one. They half-learn the new one and then continue to claim the old one was somehow "better".
Completely learn the new one. Completely delete the old one. Don't look back.
