Hi Jenny
I've been poking around looking for the big solution but so far I've nothing concrete to offer. It is interesting to note that there is a Thomas LYNEH (clearly mistranscribed Lynch!) on SP in 1851 Dundee age 18. Unfortunately he's a boarder and born Ireland...but also boarding with him amongst others is a Philip Lynch age 14 and a Mary Lynch age 20. Philip being such a wonderful name to track

I set off to prove they were brothers. I've think I've done everything but
There is a very interesting Philip in 1881 in Dundee but his age is a little young:
Dwelling: Urquhart Street
Census Place: Liff & Benvie, Forfar, Scotland
Source: FHL Film 0203482 GRO Ref Volume 282-2 EnumDist 18 Page 6
Marr Age Sex Birthplace
Philip LYNCH M 40 M Cavan Coy, Ireland
Rel: Head
Occ: Jute Factory Worker
Jane LYNCH M 35 F Fermanagh Coy, Ireland
Rel: Wife
Occ: Jute Factory Worker
Anne LYNCH U 16 F Dundee, Forfar, Scotland
Rel: Daur
Occ: Jute Factory Worker
Catherine LYNCH U 13 F Dundee, Forfar, Scotland
Rel: Daur
Occ: Jute Factory Worker
Thomas LYNCH 11 M Dundee, Forfar, Scotland
Rel: Son
Occ: Scholar
Elizabeth LYNCH 4 F Dundee, Forfar, Scotland
Rel: Daur
Philip LYNCH 1 M Dundee, Forfar, Scotland
Rel: Son
He's easy to trace though as his marriage is easily found (except he says he was 20 at marriage and 16 years later on this census he is age 40

) and so are the births of their children....these from the IGI:
1. ANN LYNCH - International Genealogical Index
Gender: Female Birth: 13 DEC 1865 Dundee, Angus, Scotland
2. JANE LYNCH - International Genealogical Index
Gender: Female Birth: 22 DEC 1871 Springburn, Lanark, Scotland
3. THOMAS LYNCH - International Genealogical Index
Gender: Male Birth: 09 APR 1870 Springburn, Lanark, Scotland
4. ELIZABETH LYNCH - International Genealogical Index
Gender: Female Birth: 07 JUN 1874 Springburn, Lanark, Scotland
5. JAMES LYNCH - International Genealogical Index
Gender: Male Birth: 27 APR 1873 Springburn, Lanark, Scotland
but one thing that really struck me is how on one record their kids were all born Dundee and the IGI shows them being born in Glasgow....about the same time your THomas was living in Glasgow with Margaret and wee Thomas. Just an illustration to show that places of birth can easily lead you astray!
I've even proven Philip's father was named Michael but that's where things go kahflooey.....there is another couple having babies in Glasgow (even one in 1855) with the same names as Philips parents and then this same couple is found living in Dundee in 1871 when Philip is in Glasgow.

Except Philip's father was dead in 1865 so it can't be them..... So very confusing and probably no connection....but there seems to be a lot of movement between Ireland, Dundee, and Glasgow and the surname LYNCH.
Not sure why I'm bothering to tell you all this as it doesn't amount to a hill of beans
I'm wondering if you've managed to trace a death of Thomas? Don't suppose any parents names were given??
Best wishes
Jean