Ok here whats going on:

void attribute((weak)) GCode_32(GCode* com) {

bool ok = Leveling::execute_G32(com);

if (ok && Motion1::homeDir[Z_AXIS] > 0 && ZProbe != nullptr && !Printer::breakLongCommand) {

bool oldDistortion = Leveling::isDistortionEnabled();

Leveling::setDistortionEnabled(false);

// we need to measure top as well to get correct height after homing

// Solution is simple and robust. We just home Z go to middle and measure

// and measure z distance with probe. Difference between z and measured z is z max error.

Motion1::homeAxes(axisBits[Z_AXIS]);

float zTheroetical = ZProbeHandler::optimumProbingHeight(), zMeasured = 0;

Motion1::setTmpPositionXYZ((Motion1::minPosOff[X_AXIS] + Motion1::maxPosOff[X_AXIS]) * 0.5,

(Motion1::minPosOff[Y_AXIS] + Motion1::maxPosOff[Y_AXIS]) * 0.5, zTheroetical);

ok = Motion1::moveByOfficial(Motion1::tmpPosition, Motion1::moveFeedrate[X_AXIS], false);

if (ok) {

ZProbeHandler::activate();

zMeasured = ZProbeHandler::runProbe();

ZProbeHandler::deactivate();

ok = zMeasured != ILLEGAL_Z_PROBE;

}

if (ok) {

Motion1::maxPos[Z_AXIS] += zMeasured - zTheroetical + (Leveling::isDistortionEnabled() ? Leveling::distortionAt(Motion1::currentPositionTransformed[X_AXIS], Motion1::currentPositionTransformed[Y_AXIS]) : 0);

EEPROM::markChanged();

Motion1::updateRotMinMax();

Motion1::currentPosition[Z_AXIS] = zMeasured;

Motion1::updatePositionsFromCurrent();

Motion2::setMotorPositionFromTransformed();

}

Leveling::setDistortionEnabled(oldDistortion);

}

if (!ok) {

GCode::fatalError(PSTR("Leveling failed!"));

}

}

You see special handling for zmax homing.

2. G32 S2: Starts with Homing, which was not like that in the older versions of repetier firmware. if that is intended, that's fine for me. I will simply delete G28 from my code.
Intentional. For safety to make sure we measure with good condition and not with some assumed but wrong coordinates.

3. It probes three points as expected.
That is the real measurement.

4. It moves up (like homing with retest)
Yes special case z max homing. You see it starts with z homing. This is to compute correct z max position which depend on rotation as well.

5. It moves to somewhere to the center and down
Yes, idea was center of bed should be safe for all printers to measure.

6. It starts a Homing in x and y direction
Thats wrong. It should only activate probe where it is and then start probing. See after description.
7. It starts to probe something starting from home position.
Ok that is expected.

Ok here activate code in zprobe.cpp

void ZProbeHandler::activate() {

if (activated) {

return;

}

// Ensure x and y positions are valid

if (!Motion1::isAxisHomed(X_AXIS) || !Motion1::isAxisHomed(Y_AXIS)) {

Motion1::homeAxes((Motion1::isAxisHomed(X_AXIS) ? 0 : 1) + (Motion1::isAxisHomed(Y_AXIS) ? 0 : 2));

}

You see there is a homing but it should only happen when x or y is not homed, which we did. But I saw illegal position again after homing so it unmarked the homing flags and starts to home xy loosing the position we wanted.Seems th ez homing is causing this:

Recv:11:18:55.825: Move CX:280.00 CY:15.00 CZ:160.00 OX:0.00 l:0.21 f:30.00

Recv:11:18:55.825: Move DX:-0.08 DE:0.00 DY:-0.07 DZ:0.17

Recv:11:18:55.825: SelectTool:0

Recv:11:18:55.881: EEPROM data updated

Recv:11:18:55.881: Warning:Move to illegal position prevented! Position should not be trusted any more!

Recv:11:18:55.881: XT:279.92 YT:14.93 ZT:160.17

Can you put back the allowedPosition debug informations from last test? XT/YT look good and ZT seems to be 160 and I assume you have the version where we added 0.01 to zmax? So not sure why it triggers now. At least with old coordinates it should not except if calibration has modified maxPos[Z_AXIS] to be lower.