All good questions mate.
Here, let me do the writers job, someone has too
The way I justify it in my head is that seeing as though the Destiny gate is supposed to be the original one (possibly built when the alterans were leaving the Ori galaxy) it is more viable to use "generic" markers as you don't know the constellations of each galaxy. So, the Seed ships go out from earth and drop these "MK1" gates across the MWG. Destiny/Seeders then head to the PG, dropping more "MK1" gates.
Now, here is where the hand held stuff comes into play. It's my thought that the reason the "MK1" gates have a limited range is due to the lack of DHD to act as a combined "second power source/targeting computer" which is why they have limited range with the "PSP's" As the Alterans map the MWG, they upgrade these old gates to the "system specific" ones and combined with the new gates/DHD's, full galactic travel becomes possible.
Alterans then at some point dial destiny, travel to the PG, rinse and repeat with even better tech.