it appears as if TR was able to get on the ballot as the Republican (much like Wallace was the Democrat in a few Deep South states in 1968) and Taft was either unwilling or unable to get on the ballot as an Independent or third party candidate.
Hiram Johnson, Roosevelt's running mate, was Governor of California. After the Republican convention in June, he became a founder of the Progressive Party, but remained a Republican. During the summer, he pointed out that state law required that a party's elector candidates be chosen by the party's candidates for the legislature chosen in the primary. At the September primary, most of the legislative candidates who were selected favored Roosevelt.
There was a procedure for an independent elector slate be qualified for the ballot, but it required a lot of signatures from persons who had not voted in the primary. So instead, voters who supported Taft had to write-in the names of 13 electors - and the use of stickers was forbidden. Apparently there was an effort to encourage Taft supporters to vote for Wilson instead of Roosevelt.
At that time, electors were individually elected. Though it was easy to vote for a party slate, it was possible to strike off individual electors. This is why Wilson got two electoral votes in California. I found a news story from late November where there were court challenges, etc. to the counting of the votes for electors, and they noted that some precinct tallies had simply marked a vote for the first candidate on a slate, and these were then being included as a vote solely for that individual.
