How Do I Level Joists for a Subfloor

Move the deck to the right, so that all main beams are continuous (move it up, to similarly simplify the notch-out, if possible). It'd make construction much easier and need less piles (especially some of those piles that would be adjacent to a tree; roots).

Red lines= entire deck moved to the right to make the beam that hits the center cutout, continuous

Blue circles= guesses as to where you need piles (assuming it's moved over to the right)

Blue line= doubled up joist to help take the weight of the notch (may or may not be necessary here, also possibly needed for the four two joists that [will] support the center cutout)

Extend the beams all the way through the triangle at the bottom, straight through its hypotenuse to the tip; one less pile there. The joist that supports that end of the triangle out in the middle of nowhere (above the 1347mm note), should probably also be doubled up.

I see no reason to double up those joists in the center, running left to right, unless that's where you're going to have a continuous seam in the decking and want them there to make the decking installation easier.

See here for how to build a deck that will last longer than your house:

2011 Porch Guide -cityofchicago.org

You don't have joists or rafters. You have engineered roof trusses. The bottom chords are 2x4 because that's all that's required for your scenario. They don't span the ceiling themselves. They're part of a rigid structure that's supported by both the top chords and the diagonal truss members. This is typical and has been standard practice since the 1970s with virtually no static failures on record.

Some trusses, in the case of very large spans or girders (which are sometimes doubled or tripled), are designed with 2x6 or 2x8 bottom chords. But for common trusses in modestly-sized homes 2x4 is standard.

The blocking was probably added to support a particular ceiling finish--tiles or wood panels, for example. Unless you have a particular need for more weight-bearing capacity, leave things alone. If you do, consult a licensed engineer who will examine things much more closely than we're able to from one shady photo.