The cost in BMP appears to be the same. However, the supply flares increase the deployment costs.
Why would I ever need to use the flares?
Supply flares vs using the IDroid supply drop
metal-gear-solid-5-the-phantom-pain
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Best Answer
While you're using the iDroid time is still running, and you remain vulnerable during that time. By contrast, flares can be thrown almost instantly.
As a result, flares are very helpful in missions where you can't just stay in one place for too long, such as boss fights.