I know the rule of thumb is to write out numbers 1–10 in words but what if the number has a decimal (i.e 3.4 million)? And if I write it as 3.4 million don’t I have to write the other numbers, for consistency, as 1 million, 2 million and so on?
If it's a measurement, or another number where precision is key, I'd prefer just numbers, possibly using powers of ten, or standard prefixes - e.g. a resistance of 3.4MΩ. Otherwise, I don't think there are any solid rules on this. Some do indeed suggest consistently writing numbers like "1 million", whereas others say "one million" for the round numbers.
Personally, I wouldn't worry too much about achieving consistency throughout an entire thesis. Focus instead on making the text flow well from one instant to the next. Maybe using words in the introduction, and numerals in later chapters would fit your thesis best? The style should be certainly be consistent within a sentence, and possibly a paragraph, to avoid confusion. However, unless you have to follow a really strict style guide no one really cares beyond that.