Flakes are not suitable for every type of fish, some are not surface feeders. Flakes are not all created equal, read the labels and compare the differences. Some have spirulina, some do not etc etc. That is why there is quite a variation in the cost of flakes.
Yes, your ground dwellers will probably clean up the waste. Depending on what the flakes are made of this may or may not be good for them. If they are not cleaned up and you have decent filtration they will end up dissolving and/or going up your filter intake.
I am sure you could make your own if you sourced the ingredients - try searching on the internet to see if it is possible. It may cost more in the long run though.