Short answer. A different law. Article 213 of the Revised Penal Code provides that when the culprit is an officer or employee of the Bureau of Internal Revenue or the Bureau of Customs, the provisions of the Administrative Code shall be applied instead of this article.
What the law says
When the culprit is an officer or employee of the Bureau of Internal Revenue or the Bureau of Customs, the provisions of the Administrative Code shall be applied.
Revised Penal Code, Article 213 — Frauds Against Public Treasury. Read the full provision →
What the law says
In his official capacity, in dealing with any person with regard to furnishing supplies, the making of contracts, or the adjustment or settlement of accounts relating to public property or funds, shall enter into an agreement with any interested party or speculator or make use of any other scheme, to defraud the Government
Revised Penal Code, Article 213 — Frauds Against Public Treasury. Read the full provision →
What the law says
Being entrusted with the collection of taxes, licenses, fees and other imposts, shall be guilty of any of the following acts or omissions
Revised Penal Code, Article 213 — Frauds Against Public Treasury. Read the full provision →
Article 213 carves out this exact situation
The article ends with a sentence written specifically for your question: when the culprit is an officer or employee of the Bureau of Internal Revenue or the Bureau of Customs, the provisions of the Administrative Code shall be applied. So Article 213 itself steps aside for a BIR or Customs officer, and directs that the Administrative Code governs instead of this article's own penalties.
What Article 213 punishes for other public officers
Outside that carve-out, Article 213 punishes a public officer who, in his official capacity, in dealing with any person with regard to furnishing supplies, the making of contracts, or the adjustment or settlement of accounts relating to public property or funds, shall enter into an agreement with any interested party or speculator or make use of any other scheme, to defraud the Government. That is the general conduct this article addresses when the officer is not from BIR or Customs.
The tax-collection scenario is where the overlap would arise
Article 213 also covers a public officer who is entrusted with the collection of taxes, licenses, fees and other imposts and commits specific abuses in that role, such as demanding more than the law authorizes or failing to issue a receipt. This is precisely the kind of function BIR and Customs officers perform, which is why the article's own final sentence exists to redirect that particular group elsewhere.
What this means for the officer you are asking about
Because the officer is with the Bureau of Internal Revenue or the Bureau of Customs, Article 213's own text takes that officer out of its coverage and points instead to the Administrative Code. Article 213 remains the governing provision for other public officers who commit the conduct it describes, but not for this specific category of officer, whose case is redirected by the article's own final sentence.
Why the article treats these two bureaus differently
Article 213 does not explain its own reasoning for singling out BIR and Customs officers, but the redirection is specific and deliberate: the article names those two bureaus by name, rather than leaving the exception open to any public officer collecting revenue. That specificity is why the answer to your question is not a general inference but something the article states outright.