Best way to clear a town?

My character/build is biotic survivor and sheltered start, as i spawned in, i went up to see the overmap, and, i had spawned two/three tiles inside a town, and had zombies, or worse banging on the front door, with more to come, could i survive, or am i screwed?

Well, with enough experience in the game, sure, you can/could survive.
As for a first/second game start… probably best to generate anew, unless you learn really fast and get lucky (and like the challenge).
You could also leave the shelter and try to flee the city.

And to answer your title:
“Fastest way” would be an atomic rocket/bomb.
“Best way” depends on your character and preferred strategy… guns, bows, traps, melee, stealth, martial arts, hit & run, death mobile, …

At the start, I usually go for stealth (don’t fight unless necessary), melee (whatever I find that does some bashing or cutting damage) and a hit & run (hit it once, run a few tiles, wait, hit it again… use the terrain to your advantage) strategy.

the bionic prepper starts with a crossbow, and a machete, with not bad skills in both, so, all i can do is open the door and start slashing

With some smart kiting you could absolutely get out, a machete is a good weapon for day one zeds. That being said, if your not confident in your combat skills, I’d focus on getting out of town, even if you draw some attention in the process. Anything that follows you all the way out, you can clear out in the fields with little risk of being ambushed by something nasty like a brute.

Did so, there was three or four zombies/tough zombies killed them, and something called a skeletal juggernaut came around the corner, are they particularly dangerous?

Well, yes… They have a lot of health, armor and cause massive damage to lightly armored survivors (see stats in the item browser).
Good thing is: You should be able to outrun them, as they are not that fast.

i managed to kite it into a basement then dragged a shelf over the stairway, closing that behind a wooden door. Also, how do i harvest plants/trees that are “in season”?

Just move next to the plant then press command ‘e’ to harvest.