Part of the confusion might be that there are two different 5 year rules.
The one used to determine if there is qualified Roth distribution is one clock per Roth account, even if the Roth account has separate sub-accounting (which is one of your Qs: it’s just an accounting). The clock starts with the first deferrals, in-plan Roth rollover or designated Roth employer contribution. Whichever is first starts the clock for determining if the earnings can be distributed tax-free. Separate accounting is used to determine when an amount can be distributed. For example, Roth deferrals generally can’t be distributed prior to 59 1/2 but an in-plan rollover might be distributable sooner, depending on the plan and the source of the rollover.
The second 5 year rule is an anti-abuse rule relating to the 10% early tax. It’s referred to as a recapture rule. The rule only applies to in-plan Roth rollovers. Normally the 10% tax is based on the amount includible in income. Roth is after-tax so the 10% tax would only apply to earnings, if it’s not a qualified distribution. But suppose I have a pre-tax account, I want an early distribution and don’t want to owe the penalty tax. I do a Roth rollover and pay normal taxes. At a later date, I then take a distribution from that account. I don’t owe the 10% penalty on the basis. Or maybe I do. Congress plugged the possible abuse by imposing the 10% penalty on the basis if the rollover was done within a 5 year period prior to the distribution. For that rule, each in-plan Roth rollover has its own 5 year period. 2010-84 Q&A 12.
I don’t see anything in SECURE 2.0 indicating that the recapture rule applies to Roth employer contributions.