Yep, should be fine. You lose a little airspace due to that speaker's larger displacement but it shouldn't audibly affect performance. JL did this with a demo vehicle a couple years back. They dropped a W7 into the stealthbox for a Subaru Legacy (2005 or 2006).
I’m also curious...was it a direct fit? I called JL audio yesterday and they’re only concern was the excursion from the W6 being longer than the W3, and wasn’t sure if there was enough clearance to the floor.
I compared the specs of the two W6 models to the 10W3V3 that came with my stealthbox and confirmed the 10W6V3 has much longer excursion than the 10W6V2 that it replaced. The JL Audio rep I spoke to was referring to the newer V3 woofer.
For anyone that might be interested down the road, I’ll try to post the comparison chart that I made.