I've studied this a bit over the years.
AFAIK (and I've looked extensively) no Japanese mfg today has a stated policy of whether MSRP includes F&S. Honda did have a stated policy back in the 70's that MSRP included F&S, but it has been withdrawn. Currently, there is no hard-core definition of what MSRP is.
Mfg's do generally provide a "freight and setup allowance" in their dealer wholesale pricing, but it is much less than most dealers attempt to charge. I view this as something between the mfg and dealer, not a consumer charge.
With the exception of BMW, no mfg adds a standard "destination charge" to the MSRP price of a motorcycle. BMW does add one but they are careful to call it a "standard destination" charge rather than a freight and setup charge so that dealers can attempt to add further F&S if they want.
Bottom line is that dealers are free to add any charge they like and they use consumer confusion to their advantage. For most bikes, they'll add $400 or so in F&S and then allow the consumer to bargain some of that away to close the sale. Bottom line is that they'll get around MSRP.
And you're free to take your business elsewhere. It's all free market supply and demand. I personally don't care if the dealer adds F&S or not, as long as the final price before TTL is market-competitive. What is market competitive varies all over the map, generally the "hot" bikes can get away with extra F&S, the slow bikes have to give up the F&S charge and often can command discounts beyond.
Hope this helps,
- Mark