If you are due back in a few weeks that extra protection probably won't apply to you. It states that a woman on maternity leave must be offered a suitable alternative role where there is one to start immediately after her existing role is made redundant.
So depending on the timings, it seems probable that you will be back from maternity leave at the crucial point. In fact, if they are hoping to have the new structure in place by September, it seems likely that you will be returning to your normal role, and then going through the application/selection process (which seems very long-drawn-out) along with everyone else. You could alter your return to work date to keep your protection longer but you must give 8 weeks' notice to do this so it's too late.
You state that you feel they are going through this restructuring to avoid their statutory responsibilities. Which responsibilities do you feel they are trying to avoid?
in terms of flexible working, if, as I understand it, you will be doing your normal job for at least a few months following your return, your flexible working application can go ahead as planned based on your current job, if that's what you still want to do. You may feel that you will stand a better chance of successfully obtaining one of the new roles if you remain on your existing hours, so you could elect to withdraw your flexible working application, go back to work on the same terms and conditions and then apply for flexible working once the dust has settled and you have hopefully successfully been appointed to one of the new roles.
In terms of applying for the new jobs on a flexible basis, you can of course do so, but if they feel the job needs to be full time in the office, there's no specific obligation on them to change those hours because one of the applicants works flexibly. If the job is so similar to your existing job, you have (at the time) existing flexible working arrangements in place that are working well and there is no reason that the 'new' job couldn't be done on the same basis, then you obviously have a stronger argument and there might possibly be an issue of discrimination at that point.