You should always set take-off power as 100% on the thrust indicators.
Changing the thrust index changes what the indicators regard as 100% thrust, but that's the indicator you always want to hit. The lower the thrust index, the lower the LP and HP rpm indication at 100% thrust indication - you can see this if you set different thrust indexes on each engine or hold the aircraft on the brakes, set 100% on the indicators, then change the thrust index.
As you noted, the information needed to do a proper FTTO (runway length vs. aircraft weight) isn't available.
So what you can accurately do is a full rated thrust takeoff, setting the maximum thrust index for the given elevation and temperature. This is what the Thrust Index tables in the JF manual and on the in-cockpit paper checklists let you set, and what will be automatically set when you click the a square on the speed reference card, along with the relevant bug speeds.
With a full rated thrust takeoff, if you've calculated the thrust index accurately, you should reach 100% thrust on the indicators with the throttles in the detent.
In a FTTO, you would advance the throttles until you registered 100% indicated thrust, which may be before the detent is reached, because you are setting the thrust index for a temperature that's much higher than reality.
The main purpose of the detent is to provide a clear throttle setting for the minimum throttle setting needing for the engines to produce rated power and the aircraft to achieve its certified performance. With the throttles in the detent and pitch matching the profile commanded by the flight director in Speed Control mode (not modelled in the JF F28), the aircraft is guaranteed to meet the requirements for obstacle avoidance etc. even on one engine.
With the throttles below the detent, this isn't guaranteed, which is why the manual says you have to advance the detent OR beyond to achieve 100% thrust when you need full rated power.
A Flexible TO is foregoing this guarantee when you have a lot of runway to spare, so you don't need to hit the detent. But if you had an engine failure after V1 you'd advance the throttle of the good engine to full thrust.
The detent also indicates/activates other things like the automatic speed brake/lift dumper retract function, and the TTC system, but it's mostly there to indicate the max rated thrust position.