Life is not easy .
You don't really give enough information to answer your question but you give plenty to confuse yourself.
Is this thing going to be single phase or do you intend to make it 3 phase? that is probably the most vital question to sort out your cut in speed.
If you want to make it 3 phase then you will have to more or less assume your waveform is a sine wave.
If you are intending to use single phase then your cut in will be determined by the peak voltage Of 50v ( half your P-P of 100V)
The peak value actually determines cut in in absolute terms ( peak higher than battery) but in real life you will do better to ignore the scope and work from the voltmeter readings. You say that the true rms and the other agree near enough so you will not be much in error using either. The fact that your voltage is not completely constant may be due to several factors, it may be mechanical in the form of speed variation or an error in the magnet spacing or similar. It may also be metering problems if the frequency is low.
Taking your 28v ac will give you about 40v peak. Your capacitor smoothed dc you say is 45v and that seems reasonable if you have voltage jitter, the capacitor will charge to the highest peak.
For normal working it looks as though you probably have a peak dc of between 40 and 45v. the scope is probably picking up little spikes on the waveform and showing peaks with little energy nearly 10v higher.
If you are intending to make this 3 phase then you will have a factor of about 1.7 on top of this to take care of the star to delta conversion.
Scopes are nice to see what is going on but are not really very useful measuring devices, the waveform will change completely when the rectifiers conduct. When you try the complete machine you will almost certainly find the absolute cut in ( few mA) comes at a lower speed than that needed for a sensible cut in of a few hundred mA. Most alternator curves show a significant toe near cut in and then a more or less straight line output with speed above sensible cut in ( 500mA to 1A)
Working from the voltmeter will be near enough, none of this is exact and I strongly suspect that none of your measurements are better than a few %. You will need a perfectly constant speed drive, perfect construction, frequencies above 50 Hz and and a perfect sine wave to get everything to agree, doesn't happen in real life.
Flux