Yes, you can use low-profile keycaps that are compatible with MX stems.
Examples include DSA profile and DSS profile, as well as the more common Cherry and DCS-profile. [Those are all taller than DSA.]
You may also wish to consider XDA and perhaps MDA profile, as they are quite flat and some of them are very cheap and attractive.
As for switches, there are many silent switches to choose from these days. The Keychron keyboards could actually make a good platform for these kind of switches. Since they can use dampening.
In the MX world, the quietest switches are Bobagum linears, U4 Boba tactiles, some cheaper OUTEMU linears + tactiles. It depends what you are looking for. They all tend to be quieter if hand-lubed.