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You were right: The servo had a slave id o as well as the ek1100. I fixed that. The error msg seems to stay the same.

wopass: load_the_modules cmd=<orig_loadrt lcec>
waitpid failed /usr/bin/rtapi_app lcec
/usr/bin/rtapi_app exited without becoming ready
insmod for lcec failed, returned -1

Shutting down and cleaning up LinuxCNC...
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments

Debug file information:
Note: Using POSIX realtime
LinuxCNC Ethercat crashed with signal 11
-- STACK TRACE START
0 /usr/lib/linuxcnc/modules/lcec.so(+0xfc8c) [0x7f3c65f33c8c]
1 /lib/x86_64-linux-gnu/libc.so.6(+0x3c050) [0x7f3c66e4d050]
2 /lib/x86_64-linux-gnu/libethercat.so.1(ecrt_slave_config_pdos+0x2f) [0x7f3c65ef752f]
3 /usr/lib/linuxcnc/modules/lcec.so(rtapi_app_main+0x40a) [0x7f3c65f34f38]
4 /usr/bin/rtapi_app(+0x10cd7) [0x5595ad189cd7]
5 /usr/bin/rtapi_app(+0x1162e) [0x5595ad18a62e]
6 /usr/bin/rtapi_app(+0x11c2c) [0x5595ad18ac2c]
7 /usr/bin/rtapi_app(+0xc974) [0x5595ad185974]
8 /usr/bin/rtapi_app(main+0x70f) [0x5595ad18544f]
9 /lib/x86_64-linux-gnu/libc.so.6(+0x2724a) [0x7f3c66e3824a]
10 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85) [0x7f3c66e38305]
11 /usr/bin/rtapi_app(_start+0x21) [0x5595ad185861]
-- STACK TRACE END
Waiting for component 'cia402' to become ready.Waited 3 seconds for master. giving up.
Note: Using POSIX realtime

5660
Stopping realtime threads
Unloading hal components
Note: Using POSIX realtime
lcec: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
motmod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
trivkins: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
homemod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
tpmod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
<commandline>:0: unloadrt failed
Note: Using POSIX realtime

This is what dmesg shows:

[ 4.277444] ec_master: loading out-of-tree module taints kernel.
[ 4.277719] ec_master: module verification failed: signature and/or required key missing - tainting kernel
[ 4.314529] EtherCAT: Master driver 1.6.4 1.6.4.g703b611-1+17.2
[ 4.314659] EtherCAT: 1 master waiting for devices.
[ 4.337595] ec_generic: EtherCAT master generic Ethernet device module 1.6.4 1.6.4.g703b611-1+17.2
[ 4.337610] EtherCAT: Accepting A0:36:9F:47:90:13 as main device for master 0.
[ 4.337624] ec_generic: Binding socket to interface 2 (enp2s0).
[ 4.360462] EtherCAT 0: Starting EtherCAT-IDLE thread.
[ 4.510128] NET: Registered PF_QIPCRTR protocol family
[ 6.785160] igb 0000:02:00.0 enp2s0: igb: enp2s0 NIC Link is Up 100 Mbps Full Duplex, Flow Control: RX
[ 6.785464] IPv6: ADDRCONF(NETDEV_CHANGE): enp2s0: link becomes ready
[ 6.792420] EtherCAT 0: Link state of ecm0 changed to UP.
[ 6.804450] EtherCAT 0: 8 slave(s) responding on main device. Re-scanning on next possibility.
[ 6.804453] EtherCAT 0: Slave states on main device: PREOP.
[ 6.804454] EtherCAT 0: Re-scanning now.
[ 6.804968] EtherCAT 0: Scanning bus.
[ 7.713258] e1000e 0000:00:1f.6 enp0s31f6: NIC Link is Up 1000 Mbps Full Duplex, Flow Control: Rx/Tx
[ 7.713306] IPv6: ADDRCONF(NETDEV_CHANGE): enp0s31f6: link becomes ready
[ 8.683950] EtherCAT 0: Bus scanning completed in 1876 ms.
[ 8.683953] EtherCAT 0: Using slave 0 as DC reference clock.
[ 192.576441] EtherCAT: Requesting master 0...
[ 192.576444] EtherCAT: Successfully requested master 0.
[ 192.576962] EtherCAT 0: Domain0: Logical address 0x00000000, 4 byte, expected working counter 6.
[ 192.576964] EtherCAT 0: Datagram domain0-0-main: Logical offset 0x00000000, 4 byte, type LRW.
[ 192.576972] EtherCAT 0: Master thread exited.
[ 192.576973] EtherCAT 0: Starting EtherCAT-OP thread.
[ 192.972388] EtherCAT 0: Slave states on main device: PREOP, OP.
[ 219.612558] EtherCAT 0: Master thread exited.
[ 219.612573] EtherCAT 0: Starting EtherCAT-IDLE thread.
[ 219.612597] EtherCAT ERROR 0-5: Failed to receive AL state datagram: Datagram initialized.
[ 219.612606] EtherCAT 0: Releasing master...
[ 219.612607] EtherCAT 0: Released.
[ 219.700744] EtherCAT 0: Slave states on main device: PREOP.
[ 219.788706] EtherCAT WARNING: Datagram 00000000c1702745 (master-fsm) was SKIPPED 1 time.
[ 1676.699770] EtherCAT: Requesting master 0...
[ 1676.699773] EtherCAT: Successfully requested master 0.
[ 1676.705131] EtherCAT 0: Releasing master...
[ 1676.705134] EtherCAT 0: Released.
[ 2530.014495] EtherCAT: Requesting master 0...
[ 2530.014498] EtherCAT: Successfully requested master 0.

I can`t really understand what`s going wrong

Can you give a bit more detail about your system, and what problem you are trying to solve, and how this will achieve that?
By "planner" I assume you mean the trajectory planner?

I am now even more confused about what's going on.
Are you actually hitting the limit switch? Or do you mean that you jog to the top soft-limit, zero the coordinate system, and then jog away again this inexplicable offset appears?

Do you have anything like external offsets enabled? Any unusual kinematics?

if you want to try i added dedicated hal pin to the spindle encoder index, you can connect it to any input pin, and you can define in the config.h and also set the active level of the signal to active low or active high.

If the original manufacturer thought that is was important enough not to require homing to go to the trouble of fitting potentimeters I would be inclined to follow their lead.
I don't think it's a difficult thing to integrate.