Yes near the bottom of the template you will see the BLF logic in the template. If you remove the {ELSE} line and the "linekey.xx.type = 0" lines for the BLFs you want your users to be able to customize themselves when the phone re-provisions it will only overwrite those BLF keys if there is something specified in 3CX.
Alternatively if those BLF keys are only to be configured through the phone interface delete the lines in the template.
With 3CX v14 this isn't needed as much though because you can configure custom speed dials and put in a descriptive name for it. You can also give the user access to manage their extension only in the 3cx management console and they can modify their BLF settings there as well.
Example below for BLF key 28
{IF blf26}
linekey.28.line = %%Line%%
linekey.28.value = %%blf26%%
linekey.28.pickup_value = %%PickupValue%%
linekey.28.type = %%DKtype%%
linekey.28.label = %%blffirstname26%% %%blflastname26%%
linekey.28.extension = %%PickupValue%%
{ELSE} <REMOVE THIS LINE>
linekey.28.type = 0 <REMOVE THIS LINE>
{ENDIF}