Do 12th board marks matter a lot in IPM IIM Indore admissions?

No, they wouldn't be holding GD and PI if it had been important to IPM IIM Indore admissions.
You must, however, also be taking the entrance exam for other programs. The following are the causes:

• The 5-year IIM Indore program is not the best or the most worthwhile route to graduation for anyone. Nobody, however, can contest the opportunities for employment and other benefits.
• It is very expensive.
• You may regret not taking additional science or social science courses during your undergraduate or graduate studies. You should always keep in mind that you can take business studies at any point in your academic career.

You should always have a plan B or C in place because, despite your best efforts, there will be a possibility that you might not be able to clear the test.