Favored

Favored carries a sense of preferred.

So may I replace 'favored' with 'preferred'?

That would depend on the whole context. Sometimes you can use them interchangeably.
The brand of tools favored/preferred by professional mechanics.
Sometimes you can't.
The conditions favored the Canadian team, who were accustomed to the cold and snow.

I gave the context in the first post.
Can I replace it?Or is there any difference whatsoever?

Probably, but I could use a little background information about the situation in order to be able to say for sure.

"Favor" means also a bet to win. If a team is favored to win, more people are betting more money that this team will win. A horse can be favored to win a race.

The Detroit Tigers (a baseball team) are favored to win the World Series (the championship) this year.

AlpheccaStars"Favor" means also a bet to win. If a team is favored to win, more people are betting more money that this team will win. A horse can be favored to win a race. The Detroit Tigers (a baseball team) are favored to win the World Series (the championship) this year.

Depending on the exact circumstances, it could mean it is preferable to choose the rooks over the queen (e.g. make a move that leads to capturing both rooks rather than a move that will lead to the capture of the queen), or it could mean that the two rooks have an advantage over the queen (e.g. White has, say, two rooks and a bishop left, while Black has his queen and a bishop).

He is not talking about any specific circumstances. He is just naming a material imbalance.
The book is quite preliminary!

In the absence of further information as to which sense of favored was meant you could take it either way, but it wouldn't change the underlying idea.
The rooks are favored (their prospects are better)
The player will favor having the rooks (prefer, because his prospects are better)