A theme is a set of named roles that elements point at. It's easy to think of it as a palette, but the names matter more than the colours in them.
How do theme colours and theme fonts work?
The colour part carries twelve slots: two text colours, two background colours, six accents, and two hyperlink colours (visited and unvisited). In a properly built deck, an element carries a pointer to a slot in place of a colour value, something like "this bar uses Accent 1". The value of Accent 1 lives in one place. Change the slot and every pointer resolves to the new value at once.
The font part carries two roles only: a heading font and a body font. That limit isn't the software running short of imagination. Two is the number of font families a slide deck should have, and the constraint is doing you a favour. If you think you need a third, you almost certainly need a different weight or size of one you already have. That gets proper treatment when you reach precision and type.
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Why is typing a hex value a problem?
Hard-typing a hex value is the commonest way a deck becomes unmaintainable, and it's worth seeing why it tempts people. The colour picker offers a slot and it offers a custom value. The custom value is right there and it's two seconds faster. On the day you type it, you can't see any difference between the two routes. The bar is the same colour either way. The difference only exists in the future, so it's invisible in the moment and expensive later.
Prayaana's deck showed the divergence clearly. Seventy-five elements displayed the old accent colour. Forty-nine of them had a hex typed onto the object, and those forty-nine appear in the override audit as their own class. The other twenty-six arrived inside charts, carrying colours from a chart style somebody had pasted in from elsewhere. Not one of the seventy-five resolved through a theme slot, so every one needed a hand visit. The chart twenty-six are the nastier half. Nothing on the slide looks wrong, and you can't edit the colour from the place you'd look first.
How do you keep colours tied to roles?
One habit prevents the whole problem, and it costs nothing. Whenever you set a colour on an object, ask yourself which of two things you're doing: choosing a colour, or choosing a role. If this bar should be the emphasis colour, whatever that ends up being, point it at an accent slot. If this specific object must be this specific value forever, whatever the brand does, you've found one of the rare legitimate hard-typed colours. Write it down in the style note so the next person knows it was deliberate.
Prayaana's repaired deck has ten such objects. All ten are documented, and the documentation is what separates an exception from a mistake.