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Setting a Jenkins startup property requires command line access. The TIMEOUT variable is immutable, defined at process startup, and cannot be changed after that. Without command line access, you can't change that variable.
With the changes included in git plugin 2.2.3 and later, checkout timeout can now be set from the user interface. The clone timeout has been adjustable for a long time.
The only operation requested in this bug report which can't yet have its timeout adjusted is the "git clean" operation. If clean is timing out for you, then you could instead uncheck the "Clean before checkout" and "Clean after checkout" boxes, and place a first build step "git clean -xfd" or "git clean -xffd" if you use submodules. Command performed as part of build steps have no timeout.