The Qur'an in ar-Ruum:30-31 says
فَأَقِمۡ وَجۡهَكَ لِلدِّينِ حَنِيفً۬اۚ فِطۡرَتَ ٱللَّهِ ٱلَّتِى فَطَرَ ٱلنَّاسَ عَلَيۡہَاۚ لَا تَبۡدِيلَ لِخَلۡقِ ٱللَّهِۚ ذَٲلِكَ ٱلدِّينُ ٱلۡقَيِّمُ وَلَـٰكِنَّ أَڪۡثَرَ ٱلنَّاسِ لَا يَعۡلَمُونَ (٣٠).
مُنِيبِينَ إِلَيۡهِ وَٱتَّقُوهُ وَأَقِيمُواْ ٱلصَّلَوٰة وَلَا تَكُونُواْ مِنَ ٱلۡمُشۡرِڪِينَ (٣١)
translated as 
Set your face to religion as a hanif, in the primordial nature from God upon which he originated mankind...(30). turning unto Him...(31).
This is consistent with other descriptions of Fitrah elsewhere in the Qur'an that refers to this natural tendency to lean towards believing in the one God .
On the other hand, the Qur'an in Yusuf:53 says
وَمَآ أُبَرِّئُ نَفۡسِىٓۚ إِنَّ ٱلنَّفۡسَ لَأَمَّارَةُۢ بِٱلسُّوٓءِ إِلَّا مَا رَحِمَ رَبِّىٓۚ إِنَّ رَبِّى غَفُورٌ۬ رَّحِيمٌ۬ (٥٣)
translated as 
But I absolve not my own soul. Surely the soul commands to evil...(53).
My question is how are we to understand this seeming difference in the message of 30:30 vs 12:53? In the former, the fitrah, the primordial nature of man, is said to lean towards the one God (and so all that is against ألسوء/evil), and the latter says that the human soul tends to call/urge towards evil.
Can there ever be a soul that urges towards evil, who, at the same time has, a primordial nature to lean towards tawhid, or vice versa?
Please could you provide evidences based on the Qur'an and hadeeth that can help explain this seeming discrepancy?
I can think of several approaches to this: that one's nature or soul is indeed good, but that it nevertheless urges towards evil (of course, taking into account the remainder of 12:53:
Save whom my Lord may show mercy...)
; that the soul and the human nature (my shortening of the concept of 'the primordial nature, from God, upon which he originated mankind') are not entirely or necessarily the same thing; and others. But I am not familiar with the scholarly thoughts on this and would be grateful for any guidance.
Thank you and جزاك الله خيرا كثيرا.
 from Nasr et al. The Study Quran. HarperCollins Publishers. 2015
 e.g. for Ibrahim: 2:135; and for Muhammad: 10:105