I don't think so.
Windows mobile doesn't recognize NTFS (should have been an add-on, if only developpers hadn't stopped producing for this platform), and Android is Linux (Debian) based, so would rather use ext2 / ext3, and of course, FAT and FAT32, that fortunately stay the common links between all worlds...
Edit : Wait, is your card really NTFS formatted ?
Windows should automatically choose FAT32 when formatting up to these sizes. I hadn't heard of Windows Mobile being able to read it. It can't read an USB disk in NTFS from Cotulla or Zeno Sloim USB host driver, for instance.
I even tried to format EXFAT32 on my HD2, with no luck. So FAT 32 only, but din't lost room in the process of formatting 64 GB in FAT32. My 32 GB card was almost full, and I earned a full 32 GB storage, so there's no visible cluster waste.
It's even much faster than the old 32 GB card (I bought one of the first that came available form Sandisk), despite the larger volume and allocation tables.
Highly recommended upgrade for people lacking room...
It's totally stable, fast and reliable.
Now your idea to format in 2 chunks is good too. Anyway, Windows Mobile could manage them, so why not ? Maybe to be tried when 128 GB cards will become available !