Using TOS/WIndows compatible partitions for exchanging data between the Atari and Linux is not as straightforward anymore as it was years ago. Nowadays Linux thoroughly validates the MBR (Master Boot Record) partition data on the root sector. This validation fails for TOS/Windows compatible media, where the MBR contains hybrid data of both Windows and TOS partitions.
This best solution is a GUID Partition Table (GPT) instead of the legacy MBR partition scheme. When partitioning with HDDRUTIL, you have the choice between creating an MBR or a GPT scheme.
For exchanging data with Linux (but also with other platforms) a GPT is the perfect choice. Linux directly supports mounting standard TOS partitions defined by a GPT scheme. No special tools, kernel configurations or mount options are required. When partitioning with HDDRUTIL, simply select TOS compatibility (not TOS/Windows, just pure TOS) and the GPT scheme. The resulting partitions can be used by TOS, MagiC or MiNT, and by Linux right away.
Linux limits the logical sector size of FAT16 partitions to 4096 bytes, which means that the maximum size of a TOS partition that Linux can handle is 256 MiB. For FAT32 partitions, which you can also create with HDDRUTIL, there is no such size limit. Note, though, that using FAT32 partitions with the Atari requires MagiC or MiNT. When partitioning, HDDRUTIL automatically creates FAT32 partitions for partition sizes >= 1 GiB. You can force a smaller partition to be a FAT32 partition by entering the "F32" partition ID manually. Remember to only manually enter partition IDs if there is a special case you want to cover. Usually it is best to just let HDDRUTIL handle everything automatically.