It's not a matter of something of multiple parts but of multi parts that can't be simplified without destroying its function. A car has multiple parts but you can remove the trunk lid or radio and it will function. An irreducible car would be the motor, driveshaft, axles, wheels and fuel source.
Without either the propeller, shaft or motor, the flagellum won't function.
Why should it have to?
Why should the TTSS come after the flagellum? It's standard evolutionary theory. Evolutionary biologist think the flagellum has been around for 2-3 billion years. The TTSS is a delivery system for pathogens to multi-celled life which, according to evo biologist have been around for just 600 million years. You're not suggesting that TTSS popped up without a purpose, evolved into the flagellum, then found its role?
I'd be interested in where you get your dates for TTSS.
Dates on soft parts that don't fossilize are difficult to establish or verify.
Another TTSS paper.
http://www.millerandlevine.com/km/evol/design2/article.html