ESP8266 keep pin states during deepsleep - ESP8266 Register configuration

Hello wvmarle,
I did some testing now and still could not solve the problem.
I could narrow down the problem though.
The MCP23017 will work as desired, it is definitely a problem that is caused by ESP8266.
I suppose that ESP8266 outputs some oscillating voltage level after entering deepsleep.
I verified the resetting behavior with ESP-12 as well as Wemos D1 Mini. I am currently bound to use GPIO3 (or D3 on Wemos D1 Mini).
I decided to use that pin because it has to be LOW during flashing anyways which greatly combines with holding reset LOW for the rest of the electronics, so I want to stick to that GPIO.
I already have a pullup resistor in my circuit, and besides that the Wemos hardware Layout also has a unique one, so when using Wemos D1 Mini I even had 5K pullup and not 10k.

I think I have to add a hardware lowpass filter to get rid of the problem, but I still don’t know why I encounter it at all.

Confirmed: MCP23017 will set its interrupt when Microcontroller is in deepsleep as desired as long as RST is not connected to GPIO0 (only pullup to 3V3).
If connected to GPIO0:
When ESP8266 enters deepsleep, approximately 1-2 seconds later(!) MCP23017 gets resetted.
This happens
-if GPIO0 is set as OUTPUT HIGH
-if GPIO0 is set as INPUT_PULLUP
before entering deepsleep.

It does have to do nothing with I2C bus, as I have been calling Wire.endTransmission() before entering deepsleep and have been probing if that function returns 0 (success).
Afterwards I did set the I2C pins of esp8266 to input_pullup just to be absolutely sure that the bus is freed.

So, my problem is that ESP8266 GPIO obviously outputs a LOW pulse after entering deepsleep.

Where it really gets me is that the reset does not happen while entering deepsleep but shortly after.

I am trying to figure out if that could be prevented somehow, and where it comes from at all.
I did google a lot about that as well, but the closest I came to an answer was this post, where somebody oscilloscoped all ESP8266 pins during run, deepsleep and restart using different pullups or none at all.
Pretty neat.
https://www.esp8266.com/viewtopic.php?f=5&t=11282
In the diagram one can see that GPIO0 only drops to approximately 2.8V when using a 10k pullup, which should not lead to a reset of an MCP23017 connected with its RST pin to GPIO0.
Besides being not sure which frequency I would have to tune a low pass filter to as a workaround (1Hz?—> needs large cap) I would still like to find out what is causing this and if I could prevent that using software.

I do not know deeply enough what else could fire a low pulse inside ESP8266 on that pin, and also the oscilloscope readings in the link above seem to have no indication that it should happen at all.
Keep in mind that the low pulse obviously happens 1 or 2s later, maybe this time stamp is not included in the oscilloscope readings.