Flight above 5000ft has (in many cases) been more honoured in the breach than the observance but with proper training I see no great difficulties. The necessary procedures, hemispheric cruising-levels, radio frequencies and monitoring, meterological considerations and navigational aspects (buffer from controlled airspace etc) should be incorporated into nav training, if not already included. If flight above 5000 feet enhances safety by reducing forced landings in inhospitable country then it is a useful gain. I have spent some time at FL140 without supplemental oxygen during my skydiving career and would not anticipate a need to exceed FL100 in the types of flying one could reasonably expect RA-Aus aircraft to do. Those wishing to exceed FL100 should carry supplemental oxygen and be trained to use it.
As far as the 600Kg MTOW weight increase, this allows a number of aircraft to now carry enough fuel to perform nav training with some of the heavier individuals who are coming to RA-Aus, possibly due to loss of medical for GA, possibly because they simply didn't fit into 152-sized training aircraft. It means an aircraft which can be certified for MTOW of 600Kg instead of 544Kg can use this increase for additional fuel so navs of reasonable duration and complexity to fully develop navigational skills and exercise the student over a suitable period of time can be achieved instead of shorter flights with frequent stops for refuelling. However, this may require a number of 544Kg MTOW aircraft to be re-certified at the increased weight, and the manufacturers may not wish to go to the expense involved in re-certification.
As far as over-water flight is concerned, it is encumbent on the pilot and crew to equip themselves appropriately for such flights, including the use of personal floatation devices and personal locator beacons operating on the 406Mhz GMDSS frequency, registered with AMSA. This applies equally to GA as well as RA-Aus aircraft. Provided the aircraft is suitable in terms of endurance and performance, and the pilot(s) are equipped with the necessary survival equipment, then flights such as Bass Strait crossings should be undertaken with a reasonable expectation of a successful outcome. However, for pilots wishing to undertake such flights, a course in basic survival-at-sea might be money well-invested. I underwent this training (and subsequent refresher training) during my time in the merchant marine but I would say I am now un-current in this and if I were to undertake such a flight I'd certainly seek some re-training in this area.
In summary, with poper training and equipment as required, all three situations should not result in any degradation of existing safety standards, and may reduce the frequency of incidents leading to an increase in safety for RA-Aus aircraft. In addition, the increase in pilot skills and knowledge will see RA-Aus pilots better-equipped for the challenges which these recent concessions will present. RA-Aus has a significant number of aircraft already well-able to fly to these new limits, it is a case of bringing the pilots up to standard.