Agree that if a system can only sort things by Account, then allowing delimiters (dashes or periods within accounts) could be helpful IF but only if, those account segments actually controlled system functions like sorting and reporting at minimum. More importantly, for requirements like you mentioned, for directing transactions to correct bank accounts.  

Agree, QB is limited on functionality. My clients all have Government contracts and grants (non-profit) so there are very strict requirements for tracking cost and revenue/funding. We use Projects with multiple levels for all Direct costs and Indirect costs must be divided into cost pools (groups of Accounts for allocations) in addition to GAAP and IRS.

Four-digit accounts are plenty when account number is strictly to define WHAT is in the account, like cash or expense. Codes like locations or banks or donors work best as a separate code to not clog up reports with hundreds of accounts.