There is no shame or embarrassment in using a Y harness for ailerons and while it is true you cannot do flaperons with it. In that case I hate flaperons anyway and I would just do build in separate and conventional dedicated flaps, no mix. There is another actually very important plus to using one over two channels and no one ever thinks about it in these types of threads and that is the simplicity of airplane assembly at the field if it is one that cannot be carried assembled.
Another scenario agine in the interest ease of assembly this occurs with some of my multi engine airplanes where one tends to run out of channels and slots and agine with my night flying multis I definitely use a Y on ailerons to have sufficient channels I us mostly the A9 nine channel radio.
So do you have to use a channel per side on ailerons absolutely not. And there is very little disadvantage other that slightly easier set up. To say I do every airplane the same all Y's or all two channels would be silly and I use both methods after carefully thinking out each new ships mission and how to carry that out.
For many of the airplanes that I do choose to use a Y, though in reality I might not actually be using a Y but instead soldered the harness up to eliminate the extra plugs creating my own Y with no additional plug and possible failure points.
There are many ways to skin a cat gphil and by learning where and when to use an appropriate method for the application you have become a better modeler for it
John