Dapilot,
1. Generally a displaced threshold is for takeoff or taxi only. Typically it doesn't meet the weight bearing requirement for a landing surface, which may involve greater loads and impact forces than an airplane imparts while taxiing or taking off. Simply put, the airplane lands harder than it takes off.
It may also be displaced due to construction, obstacles, electronic guidance reasons, surface condition, surface traffic interference, or any other number of reasons. Large airplanes shouldn't be landing on the displaced threshold, anyway. Large airplanes should be landing in the touchdown zone. When approaching to land at a runway marked with a displaced threshold, one should not land prior to the displaced threshold.
The pilot controller glossary defines the displaced threshold as a point on the runwayother than the designated beginning of the runway. The threshold is defined as the beginning of that portion of the runway useable for landing. While you may not know the reason for the displaced threshold, you need to be aware that the surface prior to the displaced threshold isn't useable for landing (but only rollout from the opposite direction).
2. Sure, you can file the destination as the alternate. But why do you want to? You don't always need an alternate. If your destination needs an alternate, and manages to meet the alternate requirements, then you can use it...some might do this for fuel purposes when stretching a trip. However, if an airport is questionable enough to require an alternate, then pick another field, or a reasonable subtitute that not only meets the letter of the law, but the spirit of the law as well.
There are cases when you may require a takeoff alternate, and the destination can serve as the takeoff alternate if it's within an hour's flying time. Sometimes it's advantageous to list your alternate as the destination and the destination as the alternate for fuel planning purposes, if the alternate lies between the departure points and the actual destination. There are ways to do this that work to your advantage, so long as you understand your limitations, and have a sound knowledge of what to expect for actual conditions.
Sometimes folks will file to the alternate and use their intended destination as the filed alternate, then switch them enroute. This is sometimes done for weather for fuel purposes. Personally, my advice is always be sure you can get in, and carry plenty of fuel. For those traveling in light airplanes, my personal rule of thumb is that it's really hard to run out of fuel if you don't burn off the bottom half of the tank.
3. You can log as PIC the time you spend as sole manipulator of the controls in an aircraft for which you are rated. Rated means category and class, and a type rating if required. If you are a private pilot with an airplane category rating and a single engine land class rating, you may log the time you spend as sole manipulator of the controls in that category and class. If that airplane requires a high performance endorsement and you don't have it, you can still log the time, because you are RATED in the airplane.
An endorsement is NOT a rating.
You may not act as pilot in command of the airplane requiring the endorsement, if you don't have the endorsement. However, you may log the time as PIC. There is a difference between acting as pilot in command, and logging pilot in command. 14 CFR 61.51 is all about writing time in your logbook, and doesn't authorize or speak to actually BEING pilot in command. Your question regards logging time, and you are able to log PIC in tailwheel airplanes, high performance airplanes, high altitude airplanes, and complex airplanes even though you don't hold an endorsement for those airplanes.
Without the endorsement, though you can log the time as PIC, you cannot ACT as PIC.
Incidentally, you can also log instrument time if you're not instrument rated...perfectly legal and acceptable, but you should be prepared to note in your logbook the circumstances under which you logged the time, and include a reference to what made it legal (eg, sole manipulator while another pilot acted as PIC, dark moonless night over featureless terrain with adequate cloud clearance and visibility, etc). The wisdom in doing so can be another matter entirely...and remember that no flight is acceptable unless it is both legal AND safe.
Good luck!