I don't know the exact reason why it was broken. If HDD partitioning issues can affect USB live media GRUB startup then something definitely isn't configured properly. Normally a USB live media should be able to boot regardless of HDD partitioning, as it shouldn't have known anything about HDDs at that time.
I'm fine about starting things over, as currently the target system hasn't any important data yet.
Actually, the target system's partitions were created and validated using DFSee, as I also intend to run ArcaOS (OS/2 based) on this system. Before replacing the board the old system also has a functional installation of it, and I encountered the same issue during preparation phase (when installing Manjaro). I tried several USB sticks and Manjaro images and managed to find one that booted (that was probably sheer luck at that time) and proceeded to install. The installed system (even with GRUB) can boot normally afterwards. My operating systems (including Linux) were managed using AIR-BOOT (which ArcaOS currently uses, with OS/2 LVM support and could boot other OSes such as Linux and Windows).
For the time being ArcaOS (OS/2 LVM, not be confused with the Linux one) has a stricter partitioning requirement that's not compatible with any partitioning tools outside DFSee, so that all actions (including formatting) done outside DFSee has to be re-validated using it. For my use case, I need to set a CHS geometry with higher sectors-per-cylinder (such as ?/255/248) as that's only way to make ArcaOS properly recognize disks above 512GB. I'm starting to suspect this (instead of BIOS) might have been the real cause of the breakage, as I noticed some OSes would misbehave under this setting (for now it's just some DOS variants, but FreeDOS worked fine anyway. Other OSes including Linux don't appear to have any issues with this), and that I never encountered this issue elsewhere (I don't run ArcaOS on these systems, so no need to perform those complicated partitioning actions involving OS/2 LVM there).
Unfortunately from my experience that setting is very fragile. I currently only know how to format FAT32 partitions with DFSee and other partitions (mainly ones that I don't intend to expose to ArcaOS) has to be formatted elsewhere. However, most other tools that involves formatting the partition, or altering the partition's boot records, are not aware of this quirk and would just slap the default, smaller geometry to it (usually ?/255/63), causing DFSee to report a non-trivial warning (geometry mismatch between disk and partition).
This warning has no effect on most other OSes as they don't use OS/2 LVM and they mainly use LBA (hence non-trivial), but could cause the ArcaOS installation to break if left unresolved (can usually be fixed via FIXPBR) as this could confuse the OS/2 LVM. So whenever I conducted such actions I'd always go back and re-check the disk until no such non-trivial warnings left.
Also, it seems even DFSee may not be able to properly handle a partition resize under such circumstance, as one time I attempted a resize of a FAT32 partition (created and formatted using DFSee) and it ended up irreversibly corrupted (inaccessible, fsck reports errors such as "block is outside filesystem" and Windows chkdsk crashes with some unknown error codes). So most of the cases I'd avoid touching anything regarding partitions once every OS has been properly installed and configured.
EDIT: I'm able to boot and install using an old Manjaro XFCE 16.10.3 image (which uses ISOLINUX). The installation procedure completed without any issues. It seems for some reasons, the GRUB boot loader incorporated in recent USB sticks is not compatible with certain configurations.
Now the question would be, is it still possible to make an ISOLINUX-based Manjaro installation in case GRUB doesn't work as intended?