Intro
As we all know, the Lahori-Ahmadis believe that Esa (see Muhammad Ali’s english quran, 1917) (As) had a biological father.  The Qadianis never argued with the Lahoris on this topic.  Since they knew that MGA was unsure as well.  It seems that MGA made many assertions on this topic.  He made many vague statements.  He even wrote with the insinuation that Esa (As) had a father as early as 1891 and 1894.  However, later in 1904, he seems to have scolded Maulvi Noorudin for holding the view that Esa (As) had a biological father and announced his belief that Esa (as) was born miraculously per the classic islamic view on the topic.  Moreover, MGA accepted the biblical view that Esa (As) had brothers and sisters as nearly as 1884.

The classical islamic view
Obviously, the classic islamic view is that Esa (as) was born miraculously, just like Adam (as). By the will of Allah.  

The Quotes

1884—” There are many fools in this world who are ever ready to be deceived by clevers. Like u see dead fly if not died long time ago or drowned in water, can be put to life again, if it is put under salt for some time. Now a clever person can easily deceive simple fellows by playing this trick to show that the flies have become alive due to my mojiza and claim himself as the Messiah of fly.” (Braheen e Ahmadiyya Vol 4 pages 551-553)

Pre-1885  “The Christians cannot stand their ground against Islam because they have taken as god a man who had a father, four brothers and two sisters, and was constantly persecuted by the Jews.” (Ruhani Khaza’in, No. 2, vol. x, p. 53)

1891  “Jesus worked with his father Joseph for 22 years as a carpenter.” (Izala Auham, footnote, p. 303)  

The Lahoris don’t quote MGA in “Mahawab-ur-Rahman (1903) (arabic and persian only books)
It is interesting to note that he Lahoris fail to quote MGA in this book, or they fail to quote him properly.  Here is the exact quote from MGA:

“And this is also a part of our belief that the birth of Jesus took place against the normal laws”.

“Either we believe that Jesus was born on the decree of God, such is the way of Allah, He creates what He pleases, When He decrees a thing He says to it, ‘To be,’ and it is. Or, God forbid, his birth was illegitimate.” (Ruhani Khaza’in, v. 19, Introduction to the book Page 17).

^^^ These are quoted here.  See page 344.

Noorudin’s confession of holding the view that Esa (as) had a biological father
Zafrullah Khan tells us in his biographical book on Noorudin as follows:

“”The birth of Jesus (as) without a father had been a somewhat controversial question. Maulawi Nur-ud- Din ra had held the view that Jesus had a father. The Promised Messiah (as), in his book Mawahibur Rahman, announced that it was part of his doctrine that Jesus (as)
had been born without a father. On reading this Maulawi Sahib (ra) discarded his view and fell into line with the view propounded by the Promised Messiah (as).  He frankly confessed this change of view in his book Nur-ud-Din.”””(see “hazratmaulvinoorudeen” by Muhammad Zafrullah Khan, 2nd edition, published in 2006, page 100).

Did Noorudin actually fall in line with the beliefs of MGA?
After MGA died in 1908, Noorudin became the Khalifa and seems to have reverted back to his old position, i.e., that Esa (as) had a biological father.  Here is a quote from the newspaper that was operated by Mahmud Ahmad:

“The reverend says that all Muslims are agreed upon this issue, except Sir Sayyid who has rejected it on rational grounds, but that no one has rejected it on the basis of the Holy Quran. However, I will go on to show that he is wrong in saying that no one has rejected it from the Holy Quran. I will prove that people have shed light on this from the Quran itself and have proved that Jesus was not born without a father, but was born like the rest of the world. What I mean to say is that there have been differences on this issue, and that some people have believed Jesus to have had a father.”

(Tashhiz al-Azhan, April 1913, pp. 165 – 170)

Muhammad Ali’s english commentary on the Quran in 1917
Upon the publishing of this book.  The Lahori-Ahmadis had solidified their position as believing that Esa (as) had a biological father.

 

The Qadianis?
Mahmud Ahmad the Qadiani side of the house seem to have went silent on this entire topic in the era of 1914 uptil the publishing of Malik Ghulam Fareed’s commentary on the Quran.

Conclusions
MGA and his team contradicted themselves all of the time.  This is simply another case of it and a cover-up job by the Ahmadi-mullahs who followed.  Obviously, MGA copied directly from Sir Syed and never acknowledged the source.  Obviously, since 1884, MGA was trying to deny the miraculous birth of Esa (as)…however, he waited til 1904 to finally make a clarification.

Additional data: https://ahmadiyyafactcheckblog.wordpress.com/2016/10/31/mga-writes-in-opposition-to-the-islamic-view-of-the-miraculous-birth-of-esa-as/