TL;DR: (probably because) the partition is marked hidden.
A dd-copied USB stick booted fine on a few machines I tried. But these were 5-10 year old desktop boxes with BIOS.
The elementary ISO is an ISOHYBRID, like pretty much every distro these days. That means the disk image is both a bootable CD and an MBR-partitioned hard disk; a clever hack. But ...
I had to install Loki multiple times, but I used the official iso file, and created a bash script, that set up my system for my needs. I suggest You do the same, just list everything You've done earlier as bash commands and run the script after installation.
This might not sound as a direct answer to how to create ISO, but still.
As far as I understand, you need ISO to create a backup of your current system. If so, you could try making a more reliable system backup via backup software such as Timeshift instead, then write backup folder to removable media/DVD/remote disk and use it later if need be.
To download using the magnet link you need an app like qBitorrent. You can easily install it with sudo apt install qbitorrent.
Regarding your other issue. It's probably related to your web browser. You should try with another one.
ok i managed to install the kernel 4.10 and nvidia 381. I turn off the dGPU with prime on the nVidia drivers, power consumption is low so ok
however, I have issue with the restart or shutdown, the system crash when i tried to do it. Same problem, i got system freeze when i'm pluging the power cable or any usb device...
this computer is so strange...
You need to try to re-download elementary OS image. I recommend using the magnet link for downloading via torrent client, this ensures that your install image will not corrupted.
For downloading via magnet link press on magnet icon (circled in red on screenshot below).
elementary OS signs its distribution iso, cf. https://elementary.io/docs/installation#verify-your-download (for elementary OS 0.4 (loki) they used sha256sum)
For older elementary versions you should check: How to verify the downloaded .iso file?
A lot of EFI/UEFI issues have been fixed in Elementary os 0.3.2, If you was not using this new update try it.
You shoudn't need to add anything to your iso. Is your linux installed without grub or not installed at all becose of grub ? Can you boot with super grub2 disk installed on a usb? if yes use boot repair from line usb or learn about rescatux witch is ...