If you say "the Colorado River" anywhere in America, they are always talking about the big long one that is actually in Colorado and 6 other states and that formed the Grand Canyon.
The Texas Colorado river is virtually unknown outside of Texas (sorry Texans) and is usually called the Texas Colorado. It was just an accident of geography by unimaginative early Spanish explorers who didn't have (or make) accurate maps too well, and yes, some of them thought the two rivers named Colorado actually connected, but they don't and never did. To add to the confusion, early Spanish explorers frequently got confused by two rivers in Texas, the Brazos and the Colorado, and at various times each was called the name of the other one until they sorted it out into the current naming convention.