It will depend on the reaction conditions. If the surface of the silicon oxide is very clean and contains silanol groups, APTES can react with these groups and form a monolayer. This monolayer will get cross-linked by the reaction of the remaining ethoxy groups which is promoted by water. Depending on the amount of water on the wafer surface one can observe a further condensation reaction of more APTES molecules resulting in the formation of a thicker layer.
In case FDTES is added at a stage when there are ethoxy or silanol groups it will probably react.
However, the vapor pressure of the FDTES is much lower than that of APTES. This might give rise to some issues with the propper reaction conditions.
If you start the reaction with APTES I'd expect it covers all reactive site. However, your reaction condition seem rather harsh.
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