The productivity modules made a lot of sense when I started implementing this a year ago when Factorio didn't support entities have their own productivity bonus. However, I still like the idea of the modules as you can put them in vanilla entities as well.
You are right that using T1 or T2 speed modules in beacons costs a lot of electricity, but that's what I do quite often. T3 modules are SO expensive, and I generally get T3 productivity first with T1 speed modules in beacons, and later upgrade the speed modules...
Of course one of the huge downsides of removing beacons and moving them inside of machines is that you lose all this granularity - being able to choose how many beacons per machine etc. I'm personally fine with it this way, and adding more variants would just flood the crafting menu with many entities with tiny differences, not to mention they would have to be visually distinct as well.