First of all, I do not think that having a signature layout is any good for its own sake. In most fields, few people (apart from your workgroup) will attend more than one of your talks and even those who will, will likely not notice the consistency of your layout¹ – unless it’s particularly memorable, which is almost certainly not a good thing². And even if somebody notices, they will likely (and hopefully) value the quality of your design more, let alone the quality of your content.
Considering the required work, there are two aspects: (1) Creating (or choosing) a layout and (2) Using the layout throughout your presentations.
Aspect 1 takes a few hours, if you are sufficiently apt with your presentation program (and it does not suck) and know some basics of graphic design (which I suppose you do, if you are asking such a question).
Mostly it’s selecting a colour scheme, one or two fonts and a default arrangement of your slides and realising them in your presentation program and in the programs you use to generate your figures.
Regarding the constraints of existing templates, remember that (unless your problems are very individual) if no templates are the way you want them, it is very likely that you should be careful what you are wishing for.
Also beware that the fact that you have to rely on (usually unknown) projectors imposes some constraints on your font and colour selections.
Aspect 2 will usually save you some time, whether you are using a prebuilt design or your own: For example, you are very likely to reuse some material – in particular figures. And if you care about your slides being consistent (which I suppose you do), you avoid spending some time in adapting colour schemes, for example. In particular, there is usually no benefit in switching designs.
From personal experience, I have spent some time in working out a design and have not regretted it yet.
¹ Just think about, how few people give horribly designed presentations and thus can be assumed not even to notice the flaws in their own presentations, let alone the qualities of your’s.
² As you should not notice good design that much.