There is a requirement for a separate accounting for NECs, pre-tax elective deferrals, Roth deferrals, rollovers, after-tax contributions, QNECs... to be able to administer vesting rules, availability for withdrawals, and tax basis among other things. There is no requirement for maintaining separate investment accounts. The rules for crediting income to each sub-account must be clear since income factors into determining taxable versus non-taxable amounts upon distribution.
The biggest pitfall is when the recordkeeping system is not capable of tracking the separate accounting (including separate basis for some of the accounts). Trying to compensate with a manual accounting process is very time consuming (no matter how proficient one's spreadsheet skills may be).