We need to understand the meaning of person under GST ACT and income tax Act so the basic question is:-

• What is meaning of person under GST Law?   Ans. As per Definition of person given u/s 2(84) of CGST Act, 2017, A person includes individuals, Hindu Undivided Family, company including government company, firm, limited liability partnership, association of persons, body of individuals, co-operative society, local authority, government including a corporation established by or under any Central, State or provincial Act, trust and artificial juridical person.

• What is meaning of person under income tax law? As per section 2(31) of Income tax Act, person includes an Individual, a Hindu Undivided Family (HUF), a Company, a Firm, an association of persons (AOP), body of individuals (BOI), whether incorporated or not, a local authority and every artificial juridical person.

• An Individual and HUF are considered separate person or not? As per above given definition of person in GST and Income tax Act, it is clear that an individual and his HUF are considered as separate person in income tax and GST. Hence Separate PAN Card is issued for HUF and separate PAN card is issued to individual whether he is karta or that HUF or not. and In case of GST also, an individual and HUF can have separate GST registration. 

• Is HUF itself forms or it need any registration? In case of family business which are run by HUF and not by any single member of HUF in owner capacity then HUF is already formed but to represent it as HUF we need to have separate PAN card for HUF. Even if there is no business we are living in HUF then it is HUF but to undertake any legal transaction in the name of HUF, we need separate PAN card of HUF. 

• What are the documents required to obtain PAN card of HUF? For ID proof, address proof and DOB proof of HUF, an affidavit made by the Karta of Hindu Undivided Family stating name, father’s name and address of all the coparceners on the date of application and copy of any ID proof (like adhaar, DL, Passport, EID, Rashan Card or any other photo ID issued by government) in the name of Karta of HUF is required. PAN card of HUF is issued in name of karta (HUF) for example Mr. Kollipara is an individual and he is also Karta of his HUF. Then name mentioned on PAN card is as below:-

PAN of Mr. Kollipara = Name- Kollipara
PAN of HUF = Name- Kollipara (HUF)

• What are the documents required for GST registration of HUF? Following documents required for GST registration of HUF;-
• Copy of PAN card;
• Photograph and PAN of Karta;
• Copy of address proof of registered office;
  • Electricity bill, water bill, landline bill etc.;
  • Copy of legal ownership document or municipal khata copy (in case of owned premises)
  • Rent agreement and No Objection Certificate (NOC) from the owner of the premises (in case of rented premises).
• Copy of bank statement or crossed cheque or first page of pass book;
• Authorized signatory –
• Photo;
• Letter of authorization.

 
 
Now coming to your question, If two businesses as mentioned in your query are separate, one of which is run by a member of HUF with personal money and other is run by HUF with family money then it is acceptable in GST and Income tax act as HUF is considered as a separate legal entity. But this should be not a false arrangement to avoid tax.