These holes are for two separate pieces, not one.
Your L5 might differs in some details from mine, but I have tried to investigate this from your photograph, the Operating & Servicing Manual and my own L5 – using a torch to see what's hiding under the saddle.. The diagram is not too informative and does not show the Locking and other screws and pins.
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Those holes hold two blocks called the Front Strips, Left-hand and Right Hand; the latter having a rebate in its upper surface, both having a row of three holes according to the diagram.
These act on the underside of the overhanging shear to prevent the front of the saddle from lifting, and the locking screw must be tapped into the Front Plate, RH.
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The smaller holes – the outer ones for the FP, LH (top on your photo) and the single one you marked with a red square, are for dowels / guide-pins set into the Plates.The RH plate is the locking one, the LH plate is held with a hexagon-headed set-screw from underneath into that tapped hole.
If you look carefully at your photo, you can just see where the plates were by very slight colour changes.
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I am not sure what the rebate in the Right-Hand Front Plate does, only that it faces upwards, to the right and the front – which would reduce the locking area.
I could not see this rebate on my lathe – though I might have replaced it wrongly having had to dismantle the machine to move home! I have noticed if I am a bit too heavy-handed engaging the feed with the tool already on the work, I cause a slight dig-in by lifting the saddle, but once hands-off the lathe runs as it should – so now use the control delicately, pinching the lever and trigger between finger-and-thumb and easing it upwards.