I will do my best to answer your questions, or at least those that I think I remotely know.
--Whether a gear is a ‘crossover’ gear or not is not that important. Also, there are differing ideas of what the term even means. What is important is that you have chain/chainring rub and you would like to have as many usable gear combinations as possible.
--No surprise that your chain rubs on the big ring when you are in a 39 x 13 gear with your 9 speed set up on a Cervelo. I have a Cervelo P2 and the same thing happens to me with my 8 speed set up. Here is why…
--One cause of your problem is your use of ‘extreme’ gear combinations. Extreme gear combos are the use of the big chainring with the big cogs or the use of the small chainring with the small cogs. In your case, that would be the 39 x 12 and the 53 x 25. When you use those combos and others close to those, the chain has to take a fairly extreme angle from the chainring to a cog that is not directly behind the chainring, but to a cog well off to the right or to the left of the chainring, as the case may be. In other words, the chain doesn’t run straight. This can cause numerous problems, one being that, in the big ring/small cog combos, the chain will rub on the big chainring. Cervelo (and a few other bikes) make this a little worse because they have very short chainstays which make the chain take a more extreme angle in these gear combos than it would on a bike with longer chainstays.
--the chain rub problem doesn’t occur in the big ring/big cog combos because the small chainring is too small to get in the way (it ‘hides’ behind the big ring). But the chain angle is still quite severe and (as in all the extreme gear combos) the drivetrain wear is greater and the shifting less smooth.
--You could in theory solve your chain rub problem by doing just what you say, moving the entire rear cassette closer to the rear wheel, but there are problems with this. First, the chain angle would improve in the small chainring/small cog combos, but would become more extreme in the big chainring/big cog combos. That means even more drivetrain wear. Next, the only way you could get the cassette closer to the rear wheel would be to grind down part of the cassette itself, as there is no spacer between the cassette and the hub (in a normal Shimano set up). You could in theory also solve the chain rub problem by getting front chainrings that are more equal in size, but then you will vastly reduce your usable gearing range. You could also elimmate the small chainring entirely, but if you have any hills or mountains in your training or races, that would be a very poor choice.
--The solution: avoid the use of your extreme gear combos—for you, the 39 x 12 and the 53 x 25. And because you have a bike with short chainstays and 9 cogs, also avoid using your 39 x 13 as well. You lose only a few gear combinations and that solution tends to be the best compromise for a situation many riders are in on their race bikes.
I hope that helps with understanding the whole mess. Good luck.
--Whether a gear is a ‘crossover’ gear or not is not that important. Also, there are differing ideas of what the term even means. What is important is that you have chain/chainring rub and you would like to have as many usable gear combinations as possible.
--No surprise that your chain rubs on the big ring when you are in a 39 x 13 gear with your 9 speed set up on a Cervelo. I have a Cervelo P2 and the same thing happens to me with my 8 speed set up. Here is why…
--One cause of your problem is your use of ‘extreme’ gear combinations. Extreme gear combos are the use of the big chainring with the big cogs or the use of the small chainring with the small cogs. In your case, that would be the 39 x 12 and the 53 x 25. When you use those combos and others close to those, the chain has to take a fairly extreme angle from the chainring to a cog that is not directly behind the chainring, but to a cog well off to the right or to the left of the chainring, as the case may be. In other words, the chain doesn’t run straight. This can cause numerous problems, one being that, in the big ring/small cog combos, the chain will rub on the big chainring. Cervelo (and a few other bikes) make this a little worse because they have very short chainstays which make the chain take a more extreme angle in these gear combos than it would on a bike with longer chainstays.
--the chain rub problem doesn’t occur in the big ring/big cog combos because the small chainring is too small to get in the way (it ‘hides’ behind the big ring). But the chain angle is still quite severe and (as in all the extreme gear combos) the drivetrain wear is greater and the shifting less smooth.
--You could in theory solve your chain rub problem by doing just what you say, moving the entire rear cassette closer to the rear wheel, but there are problems with this. First, the chain angle would improve in the small chainring/small cog combos, but would become more extreme in the big chainring/big cog combos. That means even more drivetrain wear. Next, the only way you could get the cassette closer to the rear wheel would be to grind down part of the cassette itself, as there is no spacer between the cassette and the hub (in a normal Shimano set up). You could in theory also solve the chain rub problem by getting front chainrings that are more equal in size, but then you will vastly reduce your usable gearing range. You could also elimmate the small chainring entirely, but if you have any hills or mountains in your training or races, that would be a very poor choice.
--The solution: avoid the use of your extreme gear combos—for you, the 39 x 12 and the 53 x 25. And because you have a bike with short chainstays and 9 cogs, also avoid using your 39 x 13 as well. You lose only a few gear combinations and that solution tends to be the best compromise for a situation many riders are in on their race bikes.
I hope that helps with understanding the whole mess. Good luck.