Practice a bit wider of posture (you'll see why) and also leaning forward a bit. It will reduce the noise considerably (sans 'whistle'). If not, then wad up a bit of paper and drop it more towards the front of the bowl (use your best judgment depending on the commode for that. Don't be too hasty in trying to clog it up lol). And if you can control it enough, just don't let it out as forcefully. It's pretty easy after a while to get it. It'll get easier with more growth down there also, but don't lean too far forward until then otherwise you run the risk of it shooting out... and well, yeah. Just... use discernment. Practice.
As to the other thing and I'm fully aware it's not strictly speaking sanitary, however. Take a few sandwich ziplock bags and just wrap the stuff up in paper and put it in those and then keep it wherever (cargo pants/shorts are great, or failing that a backpack compartment) and then dispose of it when safe. I'd had to do that a few times pre-T and it really wasn't a big deal. Although, tampons are really better for that because it's just the applicators and wrappers to deal with; lot less messy too. As to the noise of that... haven't you noticed seat protectors make a great deal of noise in and of themselves? That is what they'll assume is going on. But if you're still REALLY paranoid about it, get into the habit of just using a newspaper as a prop. Bonus is that you can also wrap the stuff up in some of it without wasting so much more of the bathroom tissue. Someone you know surely must still get the paper and would take no issue of you relieving them of the chore of throwing theirs out (sports pages, funnies, whatever).
Now I'm going to let you in on a "secret": almost all guys pee sitting at least once a day. Where do you think their junk is when they're dropping a bomb? Why, tucked aiming into the bowl. Why do you think that is? It's not for the fear of showing off the goods to the inconsiderate ass that barges in, I promise you. It's actually because they'd pee all over themselves, the wall or the floor otherwise. Almost everyone pees when they have a BM (it's really hard not too). So it truly is not a big deal. Nobody cares. Guys are not in the next cubicle with their ears pressed firmly to the divider to find out other men's habits. And guys with micropenis that can't clear their fly, or else those with improperly placed urethra also have to sit to pee every time (conditions which aren't all that rare. As it happens and for all intents and purposes both apply to us). Don't sweat about it so much. If a guy claims he's NEVER sat and pissed, he's lying or has super-human bladder control. Actually, I'm fairly certain the oblong shape of the modern (American by and large) commodes are due to this very reason, other than the typically round and tiny ones of many years ago... makes more room for guys to comfortably tuck into the bowl without pinching it against the rim (which I imagine was not ideal). So that's just more evidenced to how true this all really is: guys pee sitting too. They just don't talk about it much or ever. It's nothing to be critically dysphoric or paranoid about.