The L3902 is a great machine, new model but only a few changes. Neil from Messicks has a video on the changes, they're worthwhile but not ground shaking.
The 39 is the third step up - that same chassis comes with 25, 33, 39 or 4x HP. At 39hp there would be very few tasks where you'd be short of horsepower - so I personally wouldn't worry about a few HP escaping into the HST.
In my opinion HST is massively better than gear drive unless you're mowing or plowing a long straight line. Any stop/start, anything forward/reverse, anything where you need to constantly vary ground speed, an HST is better. That describes most of the tasks you do with a smaller tractor on a smaller property, to my mind. And HST still works OK for straight line dirt work, just not quite as good as gear in that situation.
Yes, you can use a clutch. And yes, people used to do that in their cars and trucks all the time. But most are automatic now because it's far more convenient, even though you lose a few HP. A tractor clutch is heavier to use than a car or truck clutch, and in my opinion you have far more situations where you need low speed and in a gear drive would be slipping the clutch. Tractor clutches in my experience (admittedly on old crappy machines) don't slip very well - so you tend to get a lurch to start.
On the Landpride packages, check with the dealer whether they'll let you upgrade. There are low end brush hogs/box blades, and heavier duty ones. The packages tend to have the light duty ones, and the usual recommendation around here is to go for the heavier ones. But the dealer may honour the "discount" baked into the package even if you get the heavier implements.
Trailers, the general recommendation is to buy a good trailer separately. The ones in packages are often not very good. In my part of the world that means Chinese-made and poorly welded, but in your part of the world it probably just means they were made to a budget - lighter deck, lighter weight axles, maybe less effective brakes. Unless you're using it very rarely I think a cheap trailer will rust and wear out/break quickly. But if you use it only to bring the tractor home, and move it place to place a couple times a year, and can keep it under cover, then it may be all you need.