The article infers he didn't have time to file the permit due to emergency circumstances which is not true.

 If he's lived there since he was 12 why didn't he file for a permit in a timely manner as this has been enacted since 2005:

"A. It shall be unlawful for any person to remove, cut down, destroy or substantially alter a tree or other protected vegetation located within the village, living or dead, in any of the following categories, unless a permit has been obtained pursuant to this chapter:"

  He waited months "so two months after it happened" after the knowledge of the potential danger to act, and didn't file for a permit.  He is a volunteer firefighter that claimed that a deceased fire Chief gave him permission before his death, which is not legal as a Fire Chief does not have the authority to do so.  

"The impact of a dismissal on the safety and welfare of the community would be significant (see CPL 170.40 [1] [g]), as would be the impact on the confidence of the public in the criminal justice system (see CPL 170.40 [1] [h]), by permitting a volunteer firefighter to avoid laws that apply to the rest of the community."

 I don't know what people expect when they think the local laws don't apply to them.

 This is why I wont live in incorporated areas.

 In most cases local government advantages outweigh the disadvantages  of state run government.  For instance Muttontown gets more revenue this way than if they were run exclusively by the state.

   "I just wanna understand who comes up with such freedom crushing rules and why"  There's two independent environmental studies regarding the arbor in and near Muttontown.  Theres also a real-estate value to foliage metric study done in the area.  Property there ranges from $895,000-$13,500,000 so property development and maintenance is a big deal.

 I imagine the following is why:
"shrubs and associated vegetation are related to the natural, scenic
and aesthetic values and the physical and visual qualities of the environment which the village is obligated to protect. Trees and such vegetation reduce noise, provide welcome shade to village residents, preserve the balance of oxygen in the air by removing carbon dioxide and fostering air quality and create a bucolic and rural atmosphere in the village, especially along the roads. Trees and such vegetation also stabilize the soil and control water pollution by preventing soil erosion and flooding, yield advantageous climatic effects and provide a natural habitat for wildlife."

"The destruction and indiscriminate removal of trees, shrubs and related vegetation disrupts the ecological balance in nature and causes increased village costs for proper drainage control, impairs the benefits of occupancy of existing residential properties and impairs the stability and value of both improved and unimproved real property in the area of the destruction and adversely affects the health, safety and general welfare of the residents of the Village of Muttontown."

 My suggestion is to implement a change to the law by utilizing Muttontowns "Proposed Legislation" process as records show it moves faster than state legislation by about 3.2 years.  

 I agree.  I could get better equity if I lived in the local incorporated "covenant" development.  I just don't want to, however I have a handful of friends that are glad to be out of the city where anything can happen to reduce their home investment.

 The only thing I ever got involved with was the incarceration in the county jail for people in violation of covenant property laws.  My tax dollars shouldn't be used to help keep up laws that I don't have input over.

He would have never had a problem,
If he had taken 10 new crisp $100.00 bills,
and palmed them off on the City ‘Inspector’ !

That’s the way MOST  Municipalities Roll.
(They learned from  H.R.C.)

 I had to appear in court 3 times but it worked.  Just have to get involved, I wont always win but I am guaranteed to lose if I stay at home with my tushy on the couch.