Sure, many thousands of people doing blind "git clone && configure && sudo make install" could be burned by a problem like this, but someone would eventually do a diff and see the problem on any project big enough to have those thousands of trusting users in the first place.
I'm not excusing these SHA-1 weaknesses, only pointing out that it won't be trivial to apply them to program source code repos no matter how cheap the attacks get.
For instance, the demonstration case for SHAttered was a pair of PDFs: humans can't reasonably inspect those to find whatever noise had to be stuffed into them to achieve the result.
I also understand that these SHA-1 weaknesses have been used to attack X.509 certificates, but there again you have a case very unlike a software code repo, where the one doing the checking isn't another programmer but a program.