yes, I do think it would look odd to use different tile under the window and you'll still have grout to contend with anyway. I don't know that much about tile, but look into whatever is the absolute best grout sealer you can get.

or do a low backsplash using the same material your countertop is, and herringbone tile above that. some people might consider that outdated, but I think it still looks good with some tile / countertop combos. I suggest redoing your windowsill in plain wood (painted white) if you went that route.

Don't use a different material there; use a better grout. There's lots of options for grout, which brand are you selecting? The installer should be versed in using different types such a premixed or an epoxy type grout.

I have been told from some tile showrooms that urethane grout will work well for kitchen backsplashes. And that epoxy is best used in showers.

I’m not sure which brand my contractor will be using. Is there one you recommend?

Ask him what he prefers to work with; not everyone is used to all the different types. Once had clients insist on epoxy grout, and the installer had never worked with it. Long story short is that he went through 3 buckets on a backsplash because he did not know how to work with it.

I am definitely not a professional but we had something similar in our kitchen. We ended up replacing the window to a larger window and carried the counter top all the way to the window on one level (acting as the window sill). I love the look and avoided having the two level look you show in your picture

Wouldn’t use a different tile under the sill.