When you stop your car follow this step:

break ---> shift your gear to N ---> handbrake ---> leave your brake ---> shift your gear to P ----> done

Then it will be no more the THUD sound

i doing this:

Brake > handbrake > shift to P > lift brake > done

From N ---> P still need to pass R right? Can you still move up without pressing brake?

Exact steps are

Press footbrake -> shift to N -> pull handbrake -> lift footbrake -> make sure the car does not roll down -> press footbrake -> shift to P

This is to make sure it is the handbrake that is keeping your car from rolling, not the gearbox P gear.

If your P gear holds your car on a slope overnight instead of your handbrake, it may become difficult to shift out of P in the morning, or it shifts out with a sound. This is because your gearbox is keeping the car from moving, not your brakes.

maybe because your car is smoking hot like the owner ? 

Correct me if I'm wrong but Myvi 1.3 do not have timing belt but uses a timing chain instead. The service of timing chain however I'm not to sure about coz my car already 130k km and no issue with timing chain.

I suggest check for this in your car :

PROIRITY (PERFORMANCE)
1. Engine oil service (do flushing-semi synthetic sufficient)
2. Gear oil
3. Air filter ('Drop-in' for more power)
4. Spark plugs (Denso Iridium for more power)
5. Fluids (radiator/brake/power steering)
6. Check disc rotor for warping (I replace use Shoji brand slotted rotors (RM200) - coz after 60k, sure got warping)
7. Brake pads (also check brake hose)
8. Check battery and alternator (for weakness)

COMFORT/ HANDLING
1. Absorber (especially rear coz it gets very soft)
2. Absorber mounting
3. Springs
4. Wheel (allignment/chamber/balancing)
5. Caliper pin (with O-ring)
6. Air-cond (refill gas, check compressor)

I may have left out a few things, but this is what I would check for...Can anyone add on anything i left out please 

may i know whats the average of myvi SE 1.5 fuel consumption do u all having ? my one keep dropping..=.=

Thanks for pointing it out, accidentally overlooked that part 

(but the enviroment will take a hit coz most of the time, the cat-con is removed.

i can understand nothing 
once i open the link my vision starts to blur 

which means it functioned as a "filter"?