In his first stint he unleashed the spygate saga because the team wouldn't make him number one driver.
This time around he is number one and has made McLaren via Zak Brown, support his Indy challenge.
Despite not driving he is still on the payroll, so if your question was rhetorical I agree with the sentiment, he should have no say in the running of the team. But since Ron Dennis is gone and there is no one else willing to tell him to shut up, drive or ship out, instead they are pampering his every desire and yes, he is manipulating the team.
This isn't the first time McLaren have been involved in Indy (they've even won the 500) and the McLaren Group is made up of three inter-related subsidiaries that cover multiple areas of technology and racing.
McLaren Group
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McLaren Applied Technologies
This is their technology division that utilises McLaren's F1 background to spread its knowledge and tech in to other areas. They helped refine GlaxoSmithKlines toothpaste production line...F1 to toothpaste.
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McLaren Racing
The F1 team and foundation upon which the McLaren Group was built. But it has never just been an F1 team. McLaren's Indy history goes back to the 1970s. Team founder Bruce McLaren entered a trio of cars in the 1970 Indy 500 for himself, Chris Amon and Denny Hulme. All F1 drivers. McLaren would go on to win two Indy 500s in 1974 and 1976. They also entered the USAC (America's top flight single seater series at the time) championship in the 70s and competed for the championship on a few occasions. All this while they were winning in F1. In 1974 they finished 2nd with Johnny Rutherford in the USAC championship, winning the Indy 500 in the process, and won the F1 championship with Emerson Fittipladi.
Their US operations also included contesting Can-Am in the 60s and 70s which was a sportscar series. They won there as well.
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McLaren Automotive
Their road/supercar division with its own sub-division;
-- McLaren GT
McLaren's GT racing program. Oversees McLaren's various sportscar and endurance endeavours around the world.
McLaren has done it and continues to do it all. They've built and raced F1 cars, Indy cars, USAC cars, sportscars and even toothpaste production lines.
One of the primary reasons behind McLaren ending their partnership with Mercedes is due to the fact that Mercedes wanted more exclusivity from McLaren as an F1 team. Merc wanted them to limit their supercar program and other racing programs while McLaren wanted to expand their wings, as they had in the 60s and 70s. Honda allowed them to do this. Can't put anything on Alonso.
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