How to change the BOM layout i.e. order and numbering?

Why don't you exclude the fasteners from the bill of materials in the Assembly?

That way they won't reserve BOM records and you won't wind up with skips in your items numbers.

You can click and drag rows to re-arrange them.  And if you have rows that you don't want to show, there are other options.  One option is to go to the part in the tree in the assembly, right-click on it and choose the Component Properties... icon, and select Exclude from bill of materials (see below).  If you don't want to do that, and still want to hide them directly in the BOM on your drawing, I'd recommend dragging the row to the bottom of the BOM first, and then Hide it instead of deleting.  By dragging it to the bottom you won't have a gap in the numbers, and by hiding it instead of deleting it you can get it back later if you want.