I have a EO Tech 516 with the raised 7mm base to Co Witness with my Troy BuIS's. Im looking at buying a Mako 5x magnifier and a Flip To The Side mount. I was told that only the EO Tech FTS mount will raise the magnifier to the right height. Can anyone help, I was looking at Larue but if it will not raise the magnifier high enough then I'll pass. $300 for the EO Tech mount is steep.

Yes, you have it correct.  No one makes the correct height for the raised height EOTechs except the EOTech FTS mount.
The LaRue EOTech magnifier mount is designed to align with non-raised height EOTechs (511, 512, 552, etc.).  If you wait, they may make another raised height mount like they did with the AimPoint magnifier pivot mount.

Thanks for the info. I guess Ill wait.

LaRue has a non-catalog mount that is the correct height; confirmed in email correspondence.

From what I found online, the Mako 5x has a 30mm tube, just like an aimpoint magnifier.  The EO Tech magnifier has a larger diameter.  IF your Mako tube diameter is 30mm, the LT649 from LaRue will fit behind your EOTech 516; I have one sitting behind my 517 (also a 7mm raised base), and it works perfectly. I much prefer LaRue's method of holding a mount to the side rather than the EO Tech way.  Oh, and a pic: