The name بِبَكَّةَ (Bakka or Becca) used in 3:96 is the ancient name for Mecca.
إِنَّ أَوَّلَ بَيْتٍ وُضِعَ لِلنَّاسِ لَلَّذِي بِبَكَّةَ مُبَارَكًا وَهُدًى لِلْعَالَمِينَ
We can confirm that by looking at the following verse which indicates that this is the location of Abraham’s shrine.
Additionally 48:24-25, further confirms that Bakka is the same location as Mecca, as this is where the prophet set out for in order to reach the Sacred Masjid to perform his Hajj pilgrimage.
If there is still any doubt, the following verse solidifies that both Becca and Mecca we are to perform Hajj to the Sacred Masjid, and if there were actually to locations then it would create a contradictory understanding of the verses of the Quran.
The Quran utilizing two names for the same location is not unique to Mecca and Becca. We see the Quran does the same thing for several other locations as well:
- Medina (9:120) & Yathrib (33:13)
- Thamud (11:67) & Al-Hijr (15:80)
- Ad (41:15) & Erum (89:7) or Dunes (46:21)
God also does this for names of people as well:
- Jacob (2:133) & Israel (2:40)
- Iblees (7:11) & Satan (2:34)
- Jonah (10:98) & Zan-Noon (The one with the N in his name) 21:87
One reason the Quran might have utilized two names for Mecca may be because some scholars attempted to irradiate any mention of Mecca, Hajj, or any religious practices they associated with Arab Muslims from the Bible, except they failed to realize that Mecca and Becca were the same location and left its mention intact in Psalm 84 in discussion about Hajj pilgrimage.
Psalm 84
1 How lovely is your dwelling place,
Lord Almighty!
2 My soul yearns, even faints,
for the courts of the Lord;
my heart and my flesh cry out
for the living God.
3 Even the sparrow has found a home,
and the swallow a nest for herself,
where she may have her young—
a place near your altar,
Lord Almighty, my King and my God.
4 Blessed are those who dwell in your house;
they are ever praising you.
5 Blessed are those whose strength is in you,
whose hearts are set on pilgrimage.
6 As they pass through the Valley of Baka,
they make it a spring;
the autumn rains also cover it with pools.
*Note: despite being a desert the valley of Mecca does occasionally flood when the rain season comes.

**Also, some translations of Pslam 84:6 twist the translation to indicate that the Valley of Baka is a place of springs (plural), but if we look at the Hebrew the word for spring is singular, and this corresponds with the Zamzam spring in Mecca. Below is a word for word breakdown of the Hebrew:

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