Ok as jessie is out and make use of 2.4 and also because you want to speed up your prestashop store there few way to make your htaccess works.
- First workaround of all create a <Directory path/to/prestashop> and putt allow override all ( but this not really a good idea)
- Second ( the best ) include every htaccess in your apache virtualhost two resons for that this is faster ( no lstat ) second more safe third you control everythin, the plause you need to modify your config every times you change your shop rules ( if you do it a lot this boring but i do it one time a year ).
Take a look at my website https://www.kingsoul.fr and try https://developers.google.com/speed/pagespeed/insights/
If you are faster let me know and post it there
Apache 2.4, prestashop 1.6