The "Force HD Textures" option is always saved automatically without having to press the "Save to FSX" button, it was obviously made this way on purpose, so you don't have to apply the other tweaks together with it.
However, it's not as if the Addon Manager would "force" different tweaks compared to the one you already have in your FSX.CFG: the settings in that page are READ FROM your FSX.CFG!
Only if there was no tweak in the first place, the Addon Manager comes with its own default values OR, if you press the "Defaults" button, all the settings will go back to default values but even in that case, they will be written back ONLY after pressing the "Save to FSX" button.
The only way for the Addon Manager to "disrupt" your tweaks, is to first press the "Default" button and THEN pressing the "Save to FSX" button, otherwise what is on that page are exactly the same values you already had in your FSX.CFG so, in your example, pressing or not the "Save to FSX" button wouldn't make any difference, it's just that it's not needed for the "Force HD texture" to work, because that one is always automatically saved and doesn't even require an FSX restart.