Here's a video and this is the blade you would want to use to get perpendicular cuts, S145 FSG (490179). Getting perpendicular cuts, even in 4" thick material, is quite possible with the Trion jigsaw and this blade.
I cut a 4" block of sapele with that setup and it was close to a finish cut in terms of quality. Perpendicular, straight, easy. Don't forget to use a splinter guard.
Trion saw is REALLY good. Most important part is the right blade. Festool makes excellent blades for thick material. S105/4 FSG (up to 3-3/8" material) and S145/4 FSG (up to 4-3/4" material)
I would also add to the above that proper techniique is important in ensuring a perpendicular cut. Don't push the blade faster than the sawdust can be cleared; you will blue the blade and get deflection. And, as in most cases in life; practice makes perfect.
I use the Trion as my primary tool to cut 4 x material, usually pressure treated lumber for decks. Using festool blades and , setting the guide as demonstrated in the video is critical to a good cut. I also use a carpenter square as a guide for a perfect perpendicular cut and a slow feed rate.
Practice with it, if you don't like it you still have the 30 day return policy.