Agreed.
The Yosemite combo updater will install on any Yosemite system, while booted to that system. You can't use an El Cap boot to run the updater for Yosemite.
Better choice, as NoBoMac neatly pointed out, is to download the Yosemite installer. You can get that directly from the App Store, assuming you have previously "purchased" Yosemite. It will be listed in the Purchases tab of your App Store.
Don't let the installer run, just download it. Then use the various methods to create a bootable installer from the Yosemite installer app. You also have the advantage of a recent download that will give you and up-to-date install of Yosemite, other than the recent security update, and a couple of apps like iTunes and Safari will also update in Yosemite.