I'm almost certain that this response will come too late for you: but I'm going to reply for anybody revisiting this post with the same sort of questions.
A-level 3D Design is a really versatile subject, which is open to interpretation much more than the other forms of art and design. How your school chooses to structure the course is entirely up to them, and every one takes a slightly different approach to interpreting the specification. It is therefore important that you ask your prospective school/s directly about the structure of their course.
Largely though, the most successful projects will explore abstract or otherwise interesting concepts spatially, visually translating these ideas into a three-dimensional way of designing. For example, you might be looking at designing an architectural piece for your final projects - but it is important that these are rooted in some sort of overarching concept (e.g. the benefits of curved, flowing design). You don't have to get too philosophical at A-level, but showing this to some extent adds that depth which helps to unlock the highest marks.
Therefore, it is entirely appropriate to select something like a scientific basis in your project, as long as the focus always comes back to design. This subject is primarily concerned with the way you visually present and develop your ideas, including generating a wide range of initial design ideas and being able to refine these down to a very focused and specific design stemming from some sort of self-set brief. This might sound like a lot, but the first year is usually dedicated to becoming used to these processes, and you will improve significantly over this time period. Aesthetics underpin everything, and although as I mentioned the decisions behind these are important, the visuals are the main focus at the end of the day.
There is room for you and your ideas if you are engineering-focused, but it is quite a heavily artistic subject as part of the art and design specification. You must come into this course ready to think artistically, and some existing skills are very useful (but not necessary as you will have time to develop). You will be sketching concepts, design proposals, and development processes - but also usually working with model-making and/or computer-aided design software. It's a really versatile course which you can mould and adjust to fit your needs.
I would thoroughly recommend taking this A-level - but be in no doubt that it is time-consuming, and is primarily art focused.