A large part of this is alignment and the shape of the end of the bolt. The engine mount bolts can be a real bear because you are putting the bolt thru that steel plate and often skid plate too, and trying to get it into the engine. Even though it may not seem like much, when you remove one of those bolts the plate sags a little. If you remove both, it's absolutely going to sag some. Which presents a real hazard to getting them aligned correctly for easy threading when you put them back in. Steel bolts, aluminum engine block. All too easy to damage things. These were never intended to be removed on a regular basis.
Bolts that are intended to be removed and replaced for maintenance or other reasons often have a bit of taper in the tip to aid in starting the threads. Bolts that are intended to be factory installed and either never removed or only for major, rare occasions often have a more square tip profile to allow maximum thread contact. You will notice this next time you work on the bike and consider the area you are working on.
Another reason is that threads are classed in three categories. External threads are A, internal are B. Classes are 1 - Loose and spin on easily, (general purpose hardware or Ikea furniture
), 2 - Best fit to allow excellent engagement and security, but still go together easily. (this is 90% of what we use) and 3 - close tolerance. (this is a friction fit where it requires some minor effort to thread things together. Used on critical components, often where safety is an issue.) More info -
LINK
One manufacturing trick that you've likely seen is to use 2A fasteners in a safety area, but also use dowel pins to maintain alignment. This way the part is assembled precisely, and the fasteners are only holding it in place, not dictating the alignment.
If the threads are not stripped out, just lightly damaged you can often chase the threads. They make thread chasing taps that are designed not to cut metal, but to smooth it back into correct shape. A poor mans thread chaser can be made by taking a bolt the correct size and pitch and cutting or filing a notch in the end that goes from the tip approximately up 5 threads at a slight angle from the center line of the bolt. The notch is to give some room for debris as you thread this into the damaged hole. If damage is not too severe the bolt will clean up the threads and allow for smooth engagement again. Like the tap or chase tap, you go in a little, back out and clean, repeat until past the damage or deep enough for the intended fastener.
This is an example of a professional thread chasing tap. You can see it looks more like a standard tap for cutting threads, with much more relief. (note to those in the trades - This is not a turbo tap, but does look very similar.) The design, like a bottom tap, is created to pull debris out of the hole, not push it forward. (A standard taper tap pushes debris forward because it is intended to be used on a thru hole.)
View attachment 63538
This is an easier type to use, intended for garage or DIY users rather than manufacturing. Note the tip shape and relief groove. You can mimic this making your own from a bolt. These are much harder steel then an average bolt and push/roll the damaged threads back into the correct shape. Sometimes the better quality of this style will be lightly heat treated.
View attachment 63540
When you run a same size tap back into a damaged hole you are going to cut some material away, cleaning up the threads in the process to allow smooth fastener engagement again. Most of the time this is minor enough to not cause an issue. However, it aways weakens the thread because there will be less secure engagement after cutting some material out of the threads.
It's hard to tell from the OP's pictures how much damage there is. It appeared to me that the threads were completely stripped out, thus my suggestion for a timesert or helicoil insert. If the threads have not been cross threaded and are only mildly damaged, it may be possible to chase the threads back into good enough condition to still be used, but as Don mentioned, using Studs instead would be a
Good Idea™.