The explorer tree doesn't support only an alphabetical order. I suggest you make use of leading numbers to get your groups sorted, such as "01 Strategy", "02 Processes" etc.
That is alphabetically correct. When you have numbers larger than 9, you need to use also double digits for numbers lower than 10: 01, 02, 03, ... 10, 11.
ARIS Script is Javascript, hence a complete programming environment with access to ARIS via an API. You can execute macros in the (fat) client or reports on the server. You can produce any output with that: ARIS Models, Word documents, PDF, Excel documents, CSV, XML... the limit is the provided API functions and the energy you invest. Obviously sorting is something you can implement in any programming language. But sorting the groups in the explorer view is not part of the API, afaik. Usually the group structure is not very important, because hardly any user works with that. Most users just navigate the models or do a search. Structuring models provide a more intuitive way to present the database contents and provide navigation starting points.
