VisualGDB references toolchains using unique IDs and versions:
Each project file contains a ToolchainID element with the toolchain ID and version
VisualGDB matches it against a list of known toolchains on this computer (see this page) and automatically loads the correct toolchain
This mechanism allows having different toolchain locations on different machines while sharing the same project file between all users.
If you would like to check in your toolchain into the your repo, you can simply move the toolchain there, and then import it into VisualGDB on each computer (click the “locate existing toolchain” link in the toolchain selector and point it to the toolchain.xml file). VisualGDB will then automatically locate it using the usual ToolchainID reference.
You can also use the Team Settings to automatically install the same toolchain on multiple computers.