Use Atmel-ICE programmer for other JTAG debugging
In theory and from a hardware point of view: Yes. The problem will be, that whatever other tool you are going to use for those "other JTAG operations" (i.e. Boundary Scan testing or JTAG-debugging of other non-Atmel MCUs) is most likely not going to support the Atmel-ICE debugger. Especially if those are commercial tools with an interest in selling their own hardware.