OK

Personally I do feel it's 2 separate 
senses, but I think it'd be OK without the 
notes or with shorter notes.

@@ -20 +20 @@
-<s_inf>JR and certain private railway operators, e.g. Seibu, Kintetsu</s_inf>
+<s_inf>used by JR, Seibu, Kintetsu, etc.</s_inf>
@@ -27 +27 @@
-<s_inf>certain private railway operators e.g. Keiō, Keikyu, Hankyū, Hanshin</s_inf>
+<s_inf>used by Keiō, Keikyu, Hankyū, Hanshin, etc.</s_inf>

I suspect this has become a bit over-detailed. How about replacing the first two senses with 
"limited express (train making reduced no. of stops, may require additional ticket)"?

Kintetsu and Hankyu are just two Kansai-based examples though, there's many more train companies that operate 特急 trains:
https://trafficnews.jp/post/80201
"大手私鉄16社の場合、特急券がいらない特急列車を運転しているのは、関東が京成電鉄、京王電鉄、東急電鉄、京急電鉄、相鉄の5社。関西は関西は南海電鉄、京阪電
鉄、阪急電鉄、阪神電鉄の4社です。このほか、東海地方の名鉄と九州の西鉄も、特急券不要の特急列車を運転しています。"

so the second sense applies to Keisei (with the exception of their "Skyliner" train), Keiou, Tokyu, Keikyu, Sotetsu, Nankai, Keihan, 
Hankyu, Hanshin, Meitetsu and Nishitetsu, but I don't think this is an exhaustive list.

@@ -20 +20 @@
-<s_inf>JR and Kintetsu lines</s_inf>
+<s_inf>JR and certain private railway operators, e.g. Seibu, Kintetsu</s_inf>
@@ -27 +27 @@
-<s_inf>Hankyu lines</s_inf>
+<s_inf>certain private railway operators e.g. Keiō, Keikyu, Hankyū, Hanshin</s_inf>

I think we need to be specific about systems.

@@ -20 +20,2 @@
-<gloss>limited express (class of train for which a a limited-express ticket is required to board)</gloss>
+<s_inf>JR and Kintetsu lines</s_inf>
+<gloss>limited express (train for which a limited-express ticket is required)</gloss>
@@ -24 +25 @@
-<xref type="see">特別急行・2</xref>
+<xref type="see" seq="1788900">特別急行・2</xref>
@@ -26 +27,2 @@
-<gloss>limited express (train that makes a limited amount of stops)</gloss>
+<s_inf>Hankyu lines</s_inf>
+<gloss>limited express (train making a limited no. of stops)</gloss>