Is there any difference if I do MBA in IIM Indore through integrated program or get into IIM Indore through CAT?

Yes, there are a lot of differences between these two courses. After your successful completion of the integrated program, you will be awarded an Integrated Diploma in Management. And after the successful completion of a postgraduate diploma, you will be awarded Post Graduate Diploma Management. 

• You will not receive an MBA degree after completion of any of these courses from IIM Indore because all the IIMs do not fall under the Universities Grant Commission Act.
• There is a great practical understanding between the PGP students as they belong from different backgrounds, different colleges, and have different kinds of work experience. 
• There is an added advantage to IPM students as they get rounded development over the period of 5 years in a business environment while the CAT exam is being cracked by 90% of the engineers.
• But the syllabus for both these courses is the same and there is no distinction. The classes, programs, and activities, and even the placements of both PGP and IPM students are conducted together. 

Hence, there are a lot of differences between the two courses like certificate and study environment, but in the end, their course structure is similar and the placements are also conducted together.