I very much doubt this MOT introduced by politicians will involve anything the class 2 wont include except perhaps a pep talk from the GP about not drinking, smoking and other vices. Go have the class 2. If you are really pedantic send the form to your GP afterwards and simply ask him what he would do that wasnt done!!
Screening makes a lot of money in private medicine but quite honestly a urine check, blood pressure check, looking in the back of the eyes and breast examination for lady pilots is all that really scores. An ECG may ground you but rarely detects something you can treat that isnt already obvious. Eyesight acuity checks wont make your eyes better.
PSA (a blood test for prostates) HbA1C (a screening test for very slight diabetes) and a virtual colonography (the gold standard to detect early bowel cancer) are worthwhile but your GP may not offer the first 2 and certainly wont offer the latter.