The tricky thing is that you will be using ~3.3 V logic levels instead of ~5 V. You need to make sure that the other components in the circuit will read the ~3.3 V logic output from the microcontroller and also won't subject the microcontroller to more than 3.3 V logic input.
I had a look at the datasheet for the TM1639, which says this (after I ran it through Google Translate:
Logic supply voltage VDD 5 V
High level input voltage VIH 0.7 VDD - VDD V
So if you were to power the TM1639 at the expected 5 V, the minimum high logic level would be 0.7 * 5 V = 3.5 V, higher than the logic level supplied by your microcontroller running at 3.3 V.
Logic level converter modules are widely available for a very low cost. Using one of these between the microcontroller and the TM1639 will ensure that your logic levels are within the specifications of the part. You might get away without the level converter, since the ~3.3 V is close to the spec, but operating out of spec is not a recipe for reliability.
The RTC should be able to run at 3.3 V, so you only need to make sure to power it at 3.3 V, not 5 V, and there's no problem there.