Having more suspension travel enables you to ride the bike faster on rougher pistes with better control, if you happen to jump the bike  you have less chance of bottoming the suspension out and will have a much more enjoyable ride on a longer trip with rough pistes. It depends on what you surfaces you wish to ride, if you are doing a more asphalt based trip then the abs model would be OK, but for more gravel pistes I would choose the non ABS version with more suspension travel every time.
To answer your question, 60mm of extra travel WILL make a difference as you increase your speed
It also appears that there are some poorly thought out design issues with the ABS model, including poor battery placement under the tank and the abs is non switchable - which for a "Paris Dakar inspired bike" is not very clever, some more info here:
Yamaha XT 660 Z Tenere with ABS? - ADVrider
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