kouliga Hi
It is always feasible and convenient to add or modify css rules/attributes in custom.css file due to the diversified characteristics/advantages it has which are also outlined in the documentation
Major reason for the same as doing modifications in other css files can have adverse impact of loosing your modifications as JA University is powered by T3 framework which has been developed with LESS:
T3 Framework is developed with LESS, the LESS files are compiled to CSS files. Each time you compile, CSS files will be overridden so we suggest you not to use CSS to customize, develop your site because when you compile, your work can be lost.