Updating system app without root and apk install in custom ROM Custom ROM in Redmi 3S
I have installed Gapps(from opengapps) using TWRP recovery. Recently, I got an update from play store for dialer app, but not for messages which released recently. Why message app doesn't received update? Do I need to flash latest Gapps to get this?
Google distributes updates in waves (based on geographical location etc.) to balance load so that may be a reason for you not getting an update right away. Additionally updates depend on your phone android version, architecture (arm vs x86, 32-bit or 64-bit) and screen resolution so that may also be a factor in getting or not getting an app update. As of now you can see all released versions of the messaging app from google on the APKMirror website:

https://www.apkmirror.com/apk/google-inc/messenger-google-inc/#description

and manually sideload the appropriate version based on your phone's specs.