The relevent env variables are set for the matrix builds, and are irrelevant to the lint build. By default the first matrix entry is applied.
"Each job included in jobs.include inherits the first value of the array that defines a matrix dimension." https://docs.travis-ci.com/user/build-stages/#Build-Stages-and-Build-Matrix-Expansion
Note the global env variables are still applied, just the matrix are excluded: https://travis-ci.org/bitcoin/bitcoin/jobs/406455565#L558
Before: <img width="755" alt="screen shot 2018-07-20 at 19 16 45" src="https://user-images.githubusercontent.com/5470/43029041-81e5fd14-8c51-11e8-9e2a-6c4bcbb36d2c.png">
After: <img width="702" alt="screen shot 2018-07-20 at 19 23 05" src="https://user-images.githubusercontent.com/5470/43029187-5ec76b28-8c52-11e8-8b03-5bee859c0d96.png">