I am sorry but i did not get your use case clearly. If i am not wrong you are not currently using HDS.
Can you briefly explain me your use case - i mean i do not want details of how you currently do it - what i want to know is what is that you want to do using HDS and we can tell you whether its possible to do it using HDS.
When we say Fragments are of same size we dont mean whole movie which needs to be played needs to be of same size - they can be of various lengths - its just that they would be broken down into smaller chunks of same size depending specially depending on Keyframe frequency so that playback is smooth and seekable. In HDS - all client side logic of how to play HDS stream is taken care by OSMF and you dont have to build your own logic to play it.
As far fragments of different sizes are concerned – we don’t support it - I mean it might turn out during fragmentation that different fragments turn out to be of different sizes due to various reasons like Discontinuity but there’s not controllable config which someone can use to force different fragment size for same input file during same fragmentation process.
I hope above information is helpful for you.