Essentially the same. Comprehensive reform and overall reform are both reforms of the whole education system or scope, so there is little difference, and some differences are nominal.
Education reform is an old-fashioned problem. Every year, the overall reform has policies, and everyone has changed from the initial incompatibility to the last habit. There are many reforms, such as college entrance examination reform, school enrollment model reform and so on. The reform of college entrance examination mode can be called overall reform or comprehensive reform, and there is little difference between them.
Therefore, there is not much difference between the overall reform of education and the comprehensive reform. Both terms are acceptable, and one of them often appears in articles.