My approach with Beethoven rubato is in most sections keep it very steady. For slow movements "placing" certain chords and melodic highlights can be useful, but generally rests and rhythm are very important for the pacing of the music.
However, in sonata form or sonata "style" movements (some rondos etc.), slight differences in tempi for different theme groups is essential. I immediately think of dolce e molto ligato in the Waldstein. This theme suffers if played exactly at an Allegro con brio, so slightly pulling it back in the transition to this theme and then slightly pushing it forward towards the closing theme is very necessary to give the theme the beauty and expression it deserves.
The challenge comes in how noticeable the transition in tempo is. If I remember correctly, Beethoven said that somewhere his metronome marking are only good for the first few measures of a piece. However, it's also said that he always played with a very strong sense of pulse. Therefore, Beethoven likely envisioned these differences in tempi, but transitioning is the most challenging part. This seems to be the hardest part of Beethoven in general. Playing with strong pulse and expression, and then transitioning into drastically contrasting material seamlessly. Think of the romantic ideal of organic growth (the Eroica is a great study of this).
In the case of the D Minor sonata's finale, the perpetuum mobile nature of the movement implies that you've got to be very rhythmic. You might consider a slightly more pressing tempo for the second theme group, pulling it back ever so slightly for the repeat and when the main motif returns. Other than that I would be very steady. The tempo differences should really only be one or two metronome notches at most. This was one of the most challenging aspects of this movement when I prepared it for a festival.