How to invert PWM signal on STM32
According to the reference manual:


  OCx polarity is software programmable using the CCxP bit in the TIMx_CCER register. It can be programmed as active high or active low.


So you need to look up the bit assignments of that register and set/clear the bit as appropriate, or look at the API for abstraction library you are using and ask it to do this, for example set the appropriate struct value documented to control inversion, or if such does not exist modify the library source or in extremity even change the hardware bit behind the library's back.

For example, since it looks like you are using the STM32F1 HAL drivers, in your instance of an TIM_OC_InitTypeDef you would set OCPolarity to either  TIM_OCPOLARITY_HIGH or TIM_OCPOLARITY_LOW.  I will refrain from guessing which you should use (easy to just try both) but as the first has a value of zero, if you have zeroed the struct to start and not yet set anything that is probably what you have, so the second is probably what would give a different result from what you have been getting.

Ordinarily for something like this, software pre-processing of the values could work, and I'm not 100% sure that cannot here, but it would be tricky as in your depicted Manchester-ish scheme the framing period of a of a hi-low is consistent, but that of a low-hi spans two different bits and varies as a result.  Besides, you already paid for the on-chip hardware inverter.  If you didn't have the hardware inverter, something that probably would work would be to approximate the signal in thirds and clock 110 or 100 sequences out the GPIO via DMA at 3x the bit rate (or using a synchronous serial peripheral).  That's also a handy solution if you ever need to do this kind of thing on pins that don't have timers.  If you don't have much else for the processor to do you could also potentially do one channel in code using semi-calibrated delays (the timing doesn't have to be all that precise).