Here are my observations:
1.I've flashed MIUITN and it does not have this problem (network loss/incoming call failure). I've compared the MD5SUM of every img file from that ROM to xiaomi.eu ROM and here's what files are different:
boot.img
cust.img
vbmeta.img
vbmeta_system.img
vendor_boot.img
super.img
2. Maybe it is only coincidence, but on MIUI China Stable and MIUITN (China based) the option for "Preferred network type" is missing and only these 2 MIUI ROMs does not have the network/calling issue. another MIUI custom ROM which I've tested - ELITE is also having this issue. I highly doubt that this could be the reason, but this gave me the below idea - point 3
3. I've substituted the super.img in xiaomi.eu ROM with the one from MIUITN (China based). flashed my marble with this "Frankeinstein" ROM and the issue is not present.
4. The modem.img files on xiaomi.eu, MIUITN, Elite and Official MIUI China are with the same MD5SUM so the issue could not be in this file
5. While using Evolution X custom ROM (around 2 days) I did not face this issue.
tl;dr - issue is somewhere in super.img according to my tests.