If the university is the approved one under the UGC guidelines and stipulations then it does not matter much as to from where you are doing a research work but what matters is actually the topic of the research and the quality of the research work which would definitely be a point wherever you go to attend an interview for seeking a job. So, in this case as PDEU, Gandhinagar is already a well known reputed educational institute, you would not have any eligibility for job problem after doing your PhD from it.
For getting a job or securing a position in the industry one must have a very good academic background as well as a good thesis work as applicable in your case. Otherwise it is very difficult to compete with the high scoring students who take lead at the counselling or job interview sessions. But there is another way to deal with it if the past academic career is not very glittering. So, first complete your PhD because it will be a gateway to get the lecturer or Assistant Professor position in the educational institutions and also some good position in the industry as some industries prefer the PhD persons for their R & D work. After completing this, one has to consider applying in various competitive exams like the entrance exams taken by the state and central administrative services, Railway services, PSUs, Banks (preferably for the commerce background people), and many others which open a path for good career lines. So, keep both the things in mind that is getting a job purely on academic merit or trying it through some competitive exam.
So go ahead with your aspirations for research work and all the best.
Knowledge is power.