I think YAB(a little)U, but I can see your point as far as MIL issues go and appreciate that you are fragile atm (read some of your thread).
I guess what's done is done and your ds loves the toy. I think you'll mellow on the fact that it's Thomas when you see him enjoying it. All the wooden sets are compatible with that one, so no worries there, although I suspect he might want Thomas wooden trains from time to time which do cost the earth and from that pov I'm with you, but you just use that to teach him that he can't have what he wants all the time/money doesn't grow on trees iyswim etc.
He will outgrow this eventually and this kind of thing is highly saleable, so when he's a bit older and moved on to whatever comes next, then sell the table and put the money away for him.
Try not to dwell on the fact that MIL went against your wishes. It's not worth wasting your feelings/energy on and making yourself unhappy over. I know she spent too much money, but if she has it to spend, then let her spend it. I used to feel this way when dh's sister buys expensive gifts for the dc, but I just let her get on with it now (I have more important things to worry about and life's too short etc) and let the children enjoy spending her money. We can't afford to, but she can and it's a major treat for them when she takes them toy shopping. It's her way of treating them and she does love them enormously, but doesn't see them often, so spoils them a bit when she does.
At the end of the day, you are his mother, and he loves you unconditionally, which is miles better than being loved for buying big presents, which is how he might view MIL. The pleasure from gifts is short-term, but the unconditional love between you and ds is life-long and can't be bought. Worth more than any train set or other expensive gift imo.