I live in Santee and ride and also hike all those trails in the north Santee hills/sycamore regularly, including the Stowe trail. I renewed my Stowe trail permit a couple weeks ago. I was quite impressed the Marines have streamlined the permit process to 1 visit. I was in and out with permit in hand in under 30 minutes so there's really no excuse now, in my opinion, to not get one if you plan to ride or hike the Stowe trail.
On the other hand, I've ridden the Stowe trail numerous times and have never seen any kind of patrol out there. How rigorously they enforce the trail permit is anybody's best guess. I'm not going to push my luck given the past history of the trail. You're more likely to get into hot water if you're riding up into other areas of the base.
As far as riding between Poway and Santee without riding the Stowe trail, I used to ride up Candygram, hike-a-bike that really steep hill at the top of high anxiety and then follow the ridge lines to the sycamore preserve and Poway. It's not a very fun ride. Lots of climbing and descending in loose cobble stones on a fire break road, it's completely exposed and, yeah, it can get miserably hot. You could also ride down high anxiety, make a right and climb out onto the next ridge if you're really a glutton for punishment. There's also another trail up the next canyon east of the Stow Trail that goes into the Sycamore canyon preserve but the County put fencing across the trail and put up signs. That and the last section climbing up to the Sycamore canyon Lakeside parking area wasn't much fun.
Officially, none of those trails in the north Santee hills/sycamore canyon are legal although that doesn't seem to stop anybody. So far, the developer that owns much of that property, various other land owners with smaller holdings and city/County officials have all been looking the other way but things could change as we've seen in other areas of the County where trails we all love suddenly get shut down and enforcement stepped up.