So I've started writing a book. It's set in present time, but is going to be interwoven with flashbacks to a few years ago to explain how the character(s) got to this scenario in present time. I was going to choose either first or third person but something weird has happened as I've jumped into the writing. I keep writing the present timeline in first person but the flashbacks in third, but its the same main character's POV. Is this gonna work as a model for the story?
I don't see why you can't do this. There is no rule saying you can't. It's all about execution, really. How well you pull it off. These things can be jarring to the reader if not done correctly. Basically, any time you change a primary element of your writing style, you need to be careful. But again, there is nothing that says you CAN'T do it at all. It's not "not allowed"; it just requires a slightly more practiced writer to pull off, just like, for example, having multiple vs. just one viewpoint character.
You could do it. How well you can do it is still TBD.
Do use new chapters for a new POV. And make sure you make it very clear what the POV in that chapter is. You are likely to confuse people too much if you use 3rd POV when the 1st person is narrating things.
Indeed, I do not see how you have the MC doing a 3rd POV at all. Do you mean the MC does 1st POV in present but also does POV in past tense not really changing to 3rd POV?