I was a bit confused by your first photos, but the manual for this AIO system makes things clear. See pages 13 to 15 on mounting details.
From them it appears the system arrives with the fans already attached to the radiator with some long screws. And this is with the FANS on the SAME side of the rad as the two necks for tubing connection. But maybe those fans were NOT pre-mounted on the rad. NOTE that the screws you show in your photo as too long and sticking out are NOT involved in fastening the fans to the rad! The pics show the fans already fastened to the bottom of the rad as they are arranged. Those HOLES in the rad FRAME you show with screws in them are where some screws come in to mount the rad to a case frame opening.
In all mounting options the bolts that fasten the FANS to the RAD are the long ones labelled B in the first parts diagram.
What you do next depends on where in your case you intend to mount the rad and fans, and they show three options.
NOTE this for all three options. The rad always is mounted with the tubing and connection necks pointed INSIDE the case. It is normally advised that a rad and fans mounted in the FRONT panel be arranged with the fans as INTAKE units to blow or suck room air through the rad into the case. If you choose to mount in a TOP case panel, then these normally are as EXHAUST fans to blow or suck air from the case out into the room. BEFORE you start changing anything, look closely at those fans on their outer frames. Usually each fan will have TWO arrows on it. One points through the frame to indicate the direction of air flow. The other points around the frame to indicate the direction of fan blade rotation. You need to know the air flow for when you arrange the fans on the rad, according to where the complete unit is mounted (as above).
1. Rad mounted either in a case front opening OR in a case TOP opening, with the FANS on the INSIDE of the rad - that is, on the same side as the tubing necks. This arrangement does NOT appear to be shown properly in the manual. Whether front or top is chosen the case has an opening for fans or a rad , and around the edge of that opening there will be pre-drilled holes. When you place the rad on the INSIDE of the case with the fans in the INSIDE of the rad, they you use the eight shorter screws marked C. Insert them from OUTSIDE the case panel through the panel holes and then into the threaded holes in the RAD frame - those same ones in your photos - and turn them into the rad holes but ,as you say, NOT very deep. The thickness of the case panel (front or top) takes up part of the length of those screws.
2. Second alternative is for a similar mounting, but with the fans on the OUTSIDE of the rad. In this case you will not be needing the short C screws. Instead you will remove the long B screws already holding the fans to the rad - see p. 13. Then you position the rad INSIDE the case top or front panel BUT also must position the FANS between the rad frame and the panel so the fans are on the OUTSIDE of the rad. See p. 14. HERE is where you need to turn the fans the right way. IF you are placing this in the FRONT panel, the fans should suck room air in then blow it though the rad before it enters the case. IF you are top mounting, then those fans should suck air from the case and through the rad before blowing it out to the room. Either way, you must line up the holes in the rad frame with the holes in the fans and the holes in the case panel. Then re-use those long screws B to pass from outside, through the panel, through the fans frame holes, and into the rad threaded holes. Tighten moderately. This time they may turn into the rad frame holes less deeply because now they are going though one additional thickness - the case panel holes.
3. Third option outlined on p. 15. SOME cases actually have metal channels on the INSIDE of the front or top case outer panel. The intent appears to be that the rad can be mounted in that channel and fastened into place there with the short C screws. Then you place the fans on the outside of the case panel, lining up their holes with panel holes (if necessary) and threaded holes in the rad frame, and use those long B screws to fasten them into place. Again, make sure to point the fans the right way.
In all of these arrangements the screws that fasten the FANS into the RAD are the long B screws. In Option 2 above those same screws fasten everything together. In the other options you use the short C screws to fasten the rad to a panel, but those screws go though the panel thickness before turning into the rad frame holes. That's why they appear too long if you do NOT have them going though a panel.