I think you're going to end up draining the matrix into the footwell whatever you do. It's still worth draining the system though, it's a good opportunity to change the coolant.
Something else worth mentioning is that you should make sure there's a good seal around the matrix when you put it back in the box, otherwise the air will pass around rather than through the matrix. The kit should come with a length of draught excluder type stuff, I think I should have used more on mine.
If you want to feel better about it have a look at the pictures in this thread about the Citroen Xantia
https://frenchcarforum.co.uk/forum/v...ic.php?t=22181 They suffered matrix failure when they were well under 10 years old. It's an 8-12 hour job on those and some of the bits never really go back properly. Both my Xantias had a leaky matrix and both got a bottle of sealant.