Having the function keys all in modifier colour is more consistent, but having them in three groups divided by colour makes them easier to hit.
But who needs a function row these days anyway? What unique functions are on there? Most programs I know that have functions on the function keys use only the leftmost and the rightmost.
I don't think that they are very good from a usability perspective: They are far above the home row, so you would have to lift your entire hand to hit them, making you lose your bearing and needing to watch the keys. They are also labelled with numbers, which don't say anything about their function, so you would either have to remember what they do in each program, or you would have to use overlays.... although, I have not seen any overlay in the last 20 years. Have you?
I think that the two columns of textual keys to the left, like on the Sun Type 5 keyboard were better. Those keys were easier to get to from the home row position and you could develop muscle memory for using them. They also had textual labels with a consistent function in every program (that supported them).
However, I still find it to be more convenient to use key combinations of the Ctrl or Command key plus a letter key, where the letter is a mnemonic, helping me to remember the function of the command. These commands are firmly established in users' minds and are there on all keyboards without the need for a non-standard Fn modifier, so I think that they should are preferred to anything else.
BTW. Wyse function keys are all in the modifier colour. Amiga function keys were all in one colour, despite being at the top like on the Model M.