does size matter
Yes ! Having been through your dilemma on recently purchasing a new bike MY advice is try the the bike out you intend to buy , really you must. As you say not all bikes are sized quite the same. Some manufacturers measure from the top of the seat tube to the middle of the bootm bracket and some do not etc etc.
A rule of thumb I believe is thus:
Standing over the bike with your feet FLAT on the ground on a typical road bike you should have one inch of clearence . On a MTB or maybe some hybrids it should be 2 to 3 inches as the bottom bracket in higher from the ground.
As a first pass at sizing , place a book between your groin and push it up until it connects with your groin . Then get a friend who knows you well

and measure from the top of the book to the floor INCLUDING the shoes you will wear whilst riding , this should give you your correct inside leg measurement .
You then measure the length of the seat stay and height of the bottom bracket from the floor and bingo . BUT sit on one before ordering . Hope that helps