You have the above correct. The service will use the cookie at C:\Windows and when you use rabbitmqctl.bat to query the status it is using the cookie in your user directory ( %USERPROFILE% ).
When the cookies don't match the error look like

C:\Program Files (x86)\RabbitMQ Server\rabbitmq_server-2.8.2\sbin>rabbitmqctl.bat status
Status of node 'rabbit@PC-FOOBAR' ...
Error: unable to connect to node 'rabbit@PC-FOOBAR': nodedown

DIAGNOSTICS
===========

nodes in question: ['rabbit@PC-FOOBAR']

hosts, their running nodes and ports:
- PC-FOOBAR: [{rabbit,49186},{rabbitmqctl30566,63150}]

current node details:
- node name: 'rabbitmqctl30566@pc-foobar'
- home dir: U:\
- cookie hash: Vp52cEvPP1PukagWi5S/fQ==

There is one more gotcha for RabbitMQ cookies on Windows... If you have a %HOMEDIR% and %HOMEPATH% environment variables (as we do in our current test environment, and sets homedir above to U:\ ), then RabbitMQ will get the cookie there and if there isn't one it makes one up and writes it there. This left me banging my head on my desk for quite a while when trying to get this working. Once I found this gotcha it was obvious the cookie files were the problem (as documented) they were just at an odd location (not documented AFAIK).
Hope this solves someones pain setting up RabbitMQ Clustering on Windows.