I doubt that honestly.
Raphinha is in his best form these days. Why would Hansi Flick decide to cut him from the starting lineup to "rest"?
It doesn't make sense while he is one of top goal contributors. Rashford will need to earn his place there. He will need to work hard to stay fit and impress the manager. I can't say he has been in his best physical shape recently.
Well from what I think it's not that Flick wants to bench Raphinha for Rashford but rather, into the season when the games becomes too much, you know that when teams are involved in too many competitions, they tend to play more games especially this period that countries will be rounding off their WC qualifiers and as such International breaks. And when this happens, when club football resumes, they start having piled up fixtures. So from that image there, Rashford will play backup to Raphinha while he Raphinha takes a rest for the time been. And you know that backup players mainly feature in not so important games.
That means he'll mostly be coming from the bench as substitute for Raphinha then sometimes start in less important matches that requires Raphinha to be rested, it's not a bad idea since it would ease the stress of Raphinha participating in numerous competitions and risk getting injured or stressed out cause of fatigue.
Asides that, he can also be rotated in other areas like the striker position, he's played that position several at Manchester United and has got more experience than Ferran Torres playing in that role so sometimes he can be used as a top 9 when Lewandowski is not very fit to play or start a match, you know Lewandowski is not younger so he can't start too often.