This is all I can find in the School Admissions Code (available here) about travel by public transport:
Distance between home and school and ease of access by public transport
2.36 In establishing their oversubscription criteria, admission authorities should take account of the time it will take to travel to school, as well as, the safety of the route, the need to encourage cycling and walking and the availability of public transport (see paragraph 1.8) in establishing their oversubscription criteria.
2.37 Distance between home and school is a clear and objective oversubscription criterion and is often used as a tie breaker in oversubscription criteria. It has the benefit of ensuring that children will not have a disproportionately long journey if access to their nearest school is not possible. Admission authorities must explain clearly how distance from home to the school will be measured including the points at the school and the child?s home from which distance is to be measured (for example, the main school gate, the front door to the home, how flats will be treated). Admission authorities must use a reliable and reasonable system which parents can easily understand. Where a child lives with parents with shared responsibility, each for part of a week, the admission authority must make clear how the ?home? address will be determined in a fair and considered way.
2.38 It is good practice to give priority to children who could reach one school (but not others) by public transport, or to children who would have a disproportionately long journey to another school if denied admission to their nearest school.
2.39 As with all oversubscription criteria admission authorities must take account of factors that might unfairly advantage or disadvantage one child compared to another. If using distance
as an oversubscription criterion, admission authorities should ensure in their admission arrangements as a whole that families who are less able to afford property nearest the school are not excluded as a result.
I haven't heard of this 45 minutes criterion - is it in your LEA's school admissions booklet? Or is it connected with the LEA's rules on help with transport costs? To be honest, I've heard too many appeals where parents have been given completely duff (mis)information by teachers and school administrators who are not as familiar with the admissions code as they pretend to be, so unless you can get a source for this 45 minutes thing I would not rely on it.
On the question of using or not using all your preferences (and remember they are preferences not choices), it can work both ways. The fewer preferences you express then - unless you can be absolutely sure of getting one of those preferences - the greater the chance that you will be allocated a school which has vacancies but which you did not name on the form. In an extreme case, parents who name only one school thinking this will 'make' the LEA give them a place at their school usually fail, as their application does not get any additional priority simply on the basis that they've made only one preference. But, in your case, naming a school which you don't really want may (I fear) work against you. You will have an uphill struggle to convince an appeal panel that it's unreasonable to expect your daughter to attend this school, given that you named it as one of your preferences, even if it was your last preference.