The lenses specified do have a flange. For the specified f=5mm this is the most common type. The search given in the page for the lens part Assembly Instructions (openflexure.org) does turn up that type for 5mm focal length. The shortest focal length for a lens of 13mm diameter that does not have a flange, as with yours, is generally the f=8mm that you have found. Searching for 5mm focal length usually turns up the right thing.
You can use the lens that you have, if you are able to edit the OpenSCAD. Your lens will sit further out of the condenser lens clip because it does not go into the hole. The simplest way to get around this is to define the condenser lens as being thicker. It will take a bit of trial and error to get it right.
Alternatively hold it with tape or even adhesive - but not super glue as it can give a white bloom on the lens.
If you are using an objective lens higher than 40x then the longer focal length condenser lens that you have may reduce the resolution that you can achieve because the illumination angle does not fill the NA of the lens. For lower magnification and the low-cost optics it will be fine.
Note: if you are making the upright version using the current release, v7.0.0 Beta1, then there is a bug in the shape of the upright condenser. The fix is in the bug notes on the Openflexure Microscope V7.0.0-beta1 released thread. It is also rectified on the current master build.