I just started delivering with GrubHub a couple days ago after being away for about a month. I am still on the old pay model. I have only seen bonus pay in the past couple days. Never saw it before my break. It seems like bonus pay is an extra amount that GrubHub kicks in to supplement pay on the orders where the customers don't tip or tip a low amount. If I take a block of deliveries where I got bonus pay, then FLAT BASE + BONUS + TIP always adds up to exactly the same number. If FLAT BASE + TIP is greater than that number, then there is no bonus pay. The target number doesn't seem to be set in stone, though. It seems like they adjust it on an hour-to-hour basis and have different target numbers for different areas. Looking at my data, I noticed that after I moved from one area to another area the target number changed. The mileage pay appears to be entirely independent.
Keep in mind, though, that GrubHub pay is extremely market dependent right now. Probably moreso even than Uber Eats. It seems that GrubHub is overhauling their pay system, so there is a lot of discrepancy between markets right now. So bonus pay might be something different in your market.