It's entirely up to your employer (effectively yourself) to determine your salary. However, in the event of an examination, Revenue would definitely be inclined to scrutinise the mileage expenses if they are so high relative to the level of salary.
For the mileage expenses to be allowable, they must be properly logged and receipted, as to the purpose and duration of the trips. see
As regards the other €2k in receipted expenses, depending on what they are, to the extent that they are already reimbursed by the flat rate allowance (i.e. diesel, servicing, train/bus fares, motorway tolls etc...), then they would not be allowable again.