Show us a photo of the spare case and the hole you are concerned with

That’s MX360guy I’m assuming he means screw 

My Bad!!
The Machinery’s Handbook explains that bolts are used to assemble to unthreaded objects, typically with the use of a nut. In comparison, screws are used to assemble objects with threads.

I  consider the case bolts as bolts, even though they don't have a nut on them. Typically a screw is something that can go into a material like wood or sheet metal, and make its own threads. In effect, the threads in the case are the nut for the bolts.

The OP said case bolt and then cover bolt had been working on the clutch ? That’s why I said screw

longer bolt a great idea
If this does not snug up I would install a helicoil

Pretty sure he meant cover bolt. He had the cover off working on the clutch. Honestly, I don't care if anyone calls it a screw or a bolt, I'm just saying what I consider a screw and a bolt. To me a screw is something like a wood screw, or drywall screw, or sheet metal screw, and a bolt is something with machine threads. But to complicate things, what about a lag bolt? It doesn't have machine threads, and it can make its own threads into wood :0)

General rule is a bolt is hex head a screw is JIS,phillips,flat Allen  

Ah. Semantics. Just about every piece of machinery has several names. Gudgeon pin, piston pin, wrist pin depending on who is saying it.
It does not matter in the grand scheme. No point in pressing it. The names are broadly interchangeable in non design engineering circles.

TLDR.  If it is designed to support in shear and tension and has a nut on the end, it is generally a bolt.
If it is not designed or required to support in shear and screws into a threaded hole, it is generally a screw.

FYI.
A bolt in a general engineering sense has a shank that is designed to support an object under shear as well as under tension.  A bolt may most often be used with a nut, but not always.  
A screw generally is meant to support an object in tension only. So if a cover has locating dowels and threaded holes, the fastener will be a screw and if not dowelled and threaded, a bolt.
A screw is usually fully threaded, but often for convenience or cost, is not fitted, and a bolt fitted in its place and called a screw.  A fully threaded screw with a nut on the end is still a screw because it is not designed to carry shear loads.
It is not the object, it is the application or the misapplication.  A fully threaded screw clamping two undoweled pieces together should never be used with a nut (yet we all do).

However the same fastener can be called a bolt or a screw whether they are fully threaded or shanked, whether they have a hex head or not. 

Confused yet?  So am I.

See it all the time on engineering drawings. If the engineers and parts logistic guys cannot agree, what chance do we have?

Semantics..... Does not matter a jot as long as everyone has a picture in their mind of the object in question.

Edit.  Back again.

Someone mentioned time sert inserts standing proud of the surface.  If you have had a time sert fitted and it is standing proud, the machinist has either not drilled and tapped the bore deep enough to accomodate the insert, or has not reamed the counterbore deep enough.
A correctly fitted timesert should be flush or very slightly below the surface.

Tomato/tomahto semantics aside, I think if it were me I would try a longer bolt/screw first, and if that doesn't work try to tap it out to the next larger size. However if it's not leaking, or just weeping, another option is to epoxy the bolt/screw into the case for appearance, and move on.

I recently replaced a steering stabilizer in my motorhome, and the bracket was completely stripped. I just tapped it out to the next larger size, and it works up perfectly.